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Membrane ion channels are the fundamental electrical components in the nervous system. Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what these proteins look like in atomic detail but do not tell us how they function. Molecular dynamics simulations have progressed to the point that we can now simulate realistic molecular assemblies to produce quantitative calculations of the thermodynamic and kinetic quantities that control function. In this review, we summarize the state of atomistic simulation methods for ion channels to understand their conduction, activation, and drug modulation mechanisms. We are at a crossroads in atomistic simulation, where long time scale observation can provide unbiased exploration of mechanisms, supplemented by biased free energy methodologies. We illustrate the use of these approaches to describe ion conduction and selectivity in voltage-gated sodium and acid-sensing ion channels. Studies of channel gating present a significant challenge, as activation occurs on longer time scales. Enhanced sampling approaches can ensure convergence on minimum free energy pathways for activation, as illustrated here for pentameric ligand-gated ion channels that are principal to nervous system function and the actions of general anesthetics. We also examine recent studies of local anesthetic and antiepileptic drug binding to a sodium channel, revealing sites and pathways that may offer new targets for drug development. Modern simulations thus offer a range of molecular-level insights into ion channel function and modulation as a learning platform for mechanistic discovery and drug development. [ABSTRACT FROM AUTHOR]

Starting with the Rayleigh charge limiting model, a slightly different approach is used to account for the well-known discrepancy that exists between the said model and experimental ESI MS data for globular proteins. It is shown using published datasets that for globular proteins, the mass density ρ exhibits a weak second-order dependence on its mass M, according to ρ(M)∝M-α, α ~ 0.14. A direct equivalence established between ESI MS and x-ray techniques suggests a minimum but critical surface tension of 15.6 ± 5.2 mN/m for the droplet at the liquid-to-gas phase transition point. The packing density factor η for globular proteins is believed to lie between 1 (very tightly packed) and 4.6 (less tight, natively packed). While the Rayleigh charge limiting model has been linked historically to the CRM (J. Chem. Phys. 49:2240-2249, 1968; Anal. Chim. Acta 406:93-104, 2000), this paper does not expressly seek to justify the CRM, but rather uses empirical data and existing knowledge across subfields to help build a consistent picture of ESI MS phenomena that might be difficult to explain otherwise. These results would be useful in molecular dynamics (MD) simulations, understanding liquid-to-gas phase transitions and in opening up new routes for cross-calibration between ESI MS, IM MS, NMR and x-ray crystallography studies.ᅟ [ABSTRACT FROM AUTHOR]

We present a fluorogenic method to visualize misfolding and aggregation of a specific protein-of-interest in live cells using structurally modulated fluorescent protein chromophores. Combining photophysical analysis, X-ray crystallography, and theoretical calculation, we show that fluorescence is triggered by inhibition of twisted-intramolecular charge transfer of these fluorophores in the rigid microenvironment of viscous solvent or protein aggregates. Bioorthogonal conjugation of the fluorophore to Halo-tag fused protein-of-interests allows for fluorogenic detection of both misfolded and aggregated species in live cells. Unlike other methods, our method is capable of detecting previously invisible misfolded soluble proteins. This work provides the first application of fluorescent protein chromophores to detect protein conformational collapse in live cells. [ABSTRACT FROM AUTHOR]

Stable square planar organocopper(III) complexes (CuNCC2, CuNCC4, and CuBN) supported by carbacorrolebased tetradentate macrocyclic ligands with NNNC coordination cores were synthesized, and their structures were elucidated by spectroscopic means including X-ray crystallographic analysis. On the basis of their distinct planar structures, X-ray absorption/ photoelectron spectroscopic features, and temperature-independent diamagnetic nature, these organocopper complexes can be preferably considered as novel organocopper(III) species. The remarkable stability of the high-valent Cu(III) states of the complexes stems from the closed-shell electronic structure derived from the peculiar NNNC coordination of the corrolemodified frameworks, which contrasts with the redox-noninnocent radical nature of regular corrole copper(II) complexes with an NNNN core. The proposed structure was supported by DFT (B3LYP) calculations. Furthermore, a π-laminated dimer architecture linked through the inner carbons was obtained from the one-electron oxidation of CuNCC4. We envisage that the precise manipulation of the molecular orbital energies and redox profiles of these organometallic corrole complexes could eventually lead to the isolation of yet unexplored high-valent metal species and the development of their organometallic reactions. [ABSTRACT FROM AUTHOR]

TYW1 is a radical S-adenosyl-L-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine to form the posttranscriptional modification, 4-demethylwyosine, in situ on transfer RNA (tRNA). Two mechanisms have been proposed for this transformation, with one of the possible mechanisms invoking a Schiff base intermediate formed between a conserved lysine residue and pyruvate. Utilizing a combination of mass spectrometry and X-ray crystallography, we have obtained evidence to support the formation of a Schiff base lysine adduct in TYW1. When 13C labeled pyruvate is used, the mass shift of the adduct matches that of the labeled pyruvate, indicating that pyruvate is the source of the adduct. Furthermore, a crystal structure of TYW1 provides visualization of the Schiff base lysine -- pyruvate adduct, which is positioned directly adjacent to the auxiliary [4Fe -- 4S] cluster. The adduct coordinates the unique iron of the auxiliary cluster through the lysine nitrogen and a carboxylate oxygen, reminiscent of how the radical SAM [4Fe -- 4S] cluster is coordinated by SAM. The structure provides insight into the binding site for tRNA and further suggests how radical SAM chemistry can be combined with Schiff base chemistry for RNA modification. [ABSTRACT FROM AUTHOR]

Two macrocyclic tetralactam receptors are shown to selectively encapsulate anionic, square-planar chloride and bromide coordination complexes of gold(III), platinum(II), and palladium(II). Both receptors have a preorganized structure that is complementary to its precious metal guest. The receptors do not directly ligate the guest metal center but instead provide an array of arene π-electron donors that interact with the electropositive metal and hydrogen-bond donors that interact with the outer electronegative ligands. This unique mode of supramolecular recognition is illustrated by six X-ray crystal structures showing receptor encapsulation of AuCl4-, AuBr4-, PtCl4-2, or Pd2Cl6-2. In organic solution, the 1:1 association constants correlate with specific supramolecular features identified in the solid state. Technical applications using these receptors are envisioned in a wide range of fields that involve precious metals, including mining, recycling, catalysis, nanoscience, and medicine. [ABSTRACT FROM AUTHOR]

A one-step, Brønsted acid catalyzed tandem reaction for the synthesis of α-(4-oxazolyl)amino esters was developed. 4-Nitrobenzenesulfonic acid was found to be an efficient catalyst for the coupling of ethyl 2-oxobut-3-ynoates with amides to provide various α-(4-oxazolyl)amino esters. The experimental and X-ray crystallographic data suggest that a series of bond-forming reactions including imine formation, intermolecular Michael addition, and intramolecular Michael addition are involved to generate both the oxazole and amino acid functionalities. [ABSTRACT FROM AUTHOR]

Catalytic modules of assembly-line polyke-tide synthases (PKSs) have previously been observed in two very different conformations -- an "extended" architecture and an "arch-shaped" architecture -- although the catalytic relevance of neither has been directly established. By the use of a fully human naive antigen-binding fragment (Fab) library, a high-affinity antibody was identified that bound to the extended conformation of a PKS module, as verified by X-ray crystallography and tandem size-exclusion chromatography -- small-angle X-ray scattering (SEC-SAXS). Kinetic analysis proved that this antibody-stabilized module conformation was fully competent for catalysis of intermodular polyketide chain translocation as well as intramodular polyketide chain elongation and functional group modification of a growing polyketide chain. Thus, the extended conformation of a PKS module is fully competent for all of its essential catalytic functions. [ABSTRACT FROM AUTHOR]

Residence time and more recently the association rate constant kon are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant kon decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization. [ABSTRACT FROM AUTHOR]

A series of bis-BN ullazine derivatives, including the parent species, were synthesized in a small number of steps from commercially available materials. X-ray crystallographic analysis revealed that bis-BN ullazines have rigid and planar frameworks. Most of the bis-BN ullazines are stable toward air and moisture. In addition, the absorption and emission bands of these ullazines are blue-shifted, compared to those of their carbonaceous ullazine analogs. [ABSTRACT FROM AUTHOR]

Conformational flexibility has been proposed to significantly affect drug properties outside rule-of-5 (Ro5) chemical space. Here, we investigated the influence of dynamically exposed polarity on cell permeability and aqueous solubility for a structurally diverse set of drugs and clinical candidates far beyond the Ro5, all of which populated multiple distinct conformations as revealed by X-ray crystallography. Efflux-inhibited (passive) Caco-2 cell permeability correlated strongly with the compounds' minimum solvent-accessible 3D polar surface areas (PSA), whereas aqueous solubility depended less on the specific 3D conformation. Inspection of the crystal structures highlighted flexibly linked aromatic side chains and dynamically forming intramolecular hydrogen bonds as particularly effective in providing "chameleonic" properties that allow compounds to display both high cell permeability and aqueous solubility. These structural features, in combination with permeability predictions based on the correlation to solvent-accessible 3D PSA, should inspire drug design in the challenging chemical space far beyond the Ro5. [ABSTRACT FROM AUTHOR]

An integrated laboratory experiment applying concepts and techniques from organic chemistry, inorganic chemistry, and instrumental analysis is presented for use in the undergraduate curriculum. This experiment highlights the synthesis, characterization, and use of tris(2-pyridylmethyl)amine (TPMA) to make complexes with different metal salts. It incorporates laboratory practices such as literature searches, multistep synthesis, reaction mechanisms, NMR spectroscopy, and X-ray crystallography. [ABSTRACT FROM AUTHOR]

Oxacalix[3]arene[3]triazine 1 bearing three electron-deficient triazine rings was designed as a molecular model to probe the effect of anion complexation on the conformation. Owing to the intrinsic nature of bridging oxygen atoms, the flexibility arising from the six aromatic units in the macrocycle, and unique intermolecular interactions, 1 gave a tight-waisted 1,3,5-alternate conformation in the solid state. Dramatic conformational changes of 1 after binding with halide anions were revealed by X-ray crystallography. The 1:3 complexation of 1 and chloride ([1•3Cl-]) led to a pyramidal conformation as a result of cooperative anion-p interaction and weak hydrogen bonding. In contrast, 1 binding with two bromides forms a 1:2 complex, and the conformation of macrocycle produced is a C3-symmetric 1,3,5-alternate one. [ABSTRACT FROM AUTHOR]

The diarylstannylene, :Sn(AriPr4)2 (AriPr4 = C6H3-2,6-(C6H3-2,6-iPr2)2), undergoes C-H metathesis with toluene, m-xylene, or mesitylene in solutions of these solvents at 80 °C. The products, [AriPr4Sn(CH2Ar)]2 (Aryl=C6H5 (1a), C6H4-3-Me (1b), C6H3-3,5-Me2(1c)) were characterized via ¹H, 13C and 119Sn NMR, UV-vis and IR spectroscopy, and by X-ray crystallography for 1a and 1b. A stoichiometric amount of the arene, AriPr4H, was also produced in these reactions. The use of EPR spectroscopy indicated the presence of a new type of one-coordinate, tin-centered radical, :ṨnAriPr4, resulting from Sn-C bond cleavage in Sn(AriPr4)2. [ABSTRACT FROM AUTHOR]

The application of nanobodies as binding partners for structure stabilization in protein X-ray crystallography is taking an increasingly important role in structural biology. However, the addition of nanobodies to the crystallization matrices might complicate the optimization of the crystallization process, which is why analytical techniques to screen and characterize suitable nanobodies are useful. Here, we show how chemical cross-linking combined with high-mass matrix-assisted laser/desorption ionization mass spectrometry can be employed as a fast screening technique to determine binding specificities of intact nanobody·membrane protein complexes. Titration series were performed to rank the binding affinity of the interacting nanobodies. To validate the mass spectrometry data, microscale thermophoresis was used, which showed binding affinities of the stronger binding nanobodies, in the low µM range. In addition, mass spectrometry provides access to the stoichiometry of the complexes formed, which enables the definition of conditions under which homogeneous complex states are present in solution. Conformational changes of the membrane protein were investigated and competitive binding experiments were used to delimit the interaction sites of the nanobodies, which is in agreement with crystal structures obtained. The results show the diversity of specifically binding nanobodies in terms of binding affinity, stoichiometry, and binding site, which illustrates the need for an analytical screening approach. [ABSTRACT FROM AUTHOR]

We report the two-step synthesis of a molecular trefoil knot in 90% overall yield through the self-assembly of a 12-component trimeric circular zinc helicate followed by ring closing metathesis of six pendant alkene chains. Both the trimeric circular helicate intermediate and the resulting trefoil knot were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography. [ABSTRACT FROM AUTHOR]

The mystery associated with catalysis by what were once regarded as protein black boxes, diminished with the X-ray crystallographic determination of the three-dimensional structures of enzyme-substrate complexes. The report that several high-resolution X-ray crystal structures of orotidine 5'-monophosphate decarboxylase (OMPDC) failed to provide a consensus mechanism for enzyme-catalyzed decarboxylation of OMP to form uridine 5'-monophosphate, therefore, provoked a flurry of controversy. This controversy was fueled by the enormous 1023-fold rate acceleration for this enzyme, which had "jolted many biochemists' assumptions about the catalytic potential of enzymes." Our studies on the mechanism of action of OMPDC provide strong evidence that catalysis by this enzyme is not fundamentally different from less proficient catalysts, while highlighting important architectural elements that enable a peak level of performance. Many enzymes undergo substrate-induced protein conformational changes that trap their substrates in solvent occluded protein cages, but the conformational change induced by ligand binding to OMPDC is incredibly complex, as required to enable the development of 22 kcal/mol of stabilizing binding interactions with the phosphodianion and ribosyl substrate fragments of OMP. The binding energy from these fragments is utilized to activate OMPDC for catalysis of decarboxylation at the orotate fragment of OMP, through the creation of a tight, catalytically active, protein cage from the floppy, open, unliganded form of OMPDC. Such utilization of binding energy for ligand-driven conformational changes provides a general mechanism to obtain specificity in transition state binding. The rate enhancement that results from the binding of carbon acid substrates to enzymes is partly due to a reduction in the carbon acid pKa that is associated with ligand binding. The binding of UMP to OMPDC results in an unusually large >12 unit decrease in the pKa = 29 for abstraction of the C-6 substrate hydrogen, due to stabilization of an enzyme-bound vinyl carbanion, which is also an intermediate of OMPDC-catalyzed decarboxylation. The protein-ligand interactions operate to stabilize the vinyl carbanion at the enzyme active site compared to aqueous solution, rather than to stabilize the transition state for the concerted electrophilic displacement of CO2 by H+ that avoids formation of this reaction intermediate. There is evidence that OMPDC induces strain into the bound substrate. The interaction between the amide side chain of Gln-215 from the phosphodianion gripper loop and the hydroxymethylene side chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion of OMP. There are no direct stabilizing interactions between dianion gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the pyrimidine ring at the decarboxylation transition state. Rather these side chains function solely to hold OMPDC in the catalytically active closed conformation. The hydrophobic side chains that line the active site of OMPDC in the region of the departing CO2 product may function to stabilize the decarboxylation transition state by providing hydrophobic solvation of this product. [ABSTRACT FROM AUTHOR]

Molecular chaperones play a central role in protein homeostasis (a.k.a. proteostasis) by balancing protein folding, quality control, and turnover. To perform these diverse tasks, chaperones need the malleability to bind nearly any "client" protein and the fidelity to detect when it is misfolded. Remarkably, these activities are carried out by only ~180 dedicated chaperones in humans. How do a relatively small number of chaperones maintain cellular and organismal proteostasis for an entire proteome? Furthermore, once a chaperone binds a client, how does it "decide" what to do with it? One clue comes from observations that individual chaperones engage in protein-protein interactions (PPIs)--both with each other and with their clients. These physical links coordinate multiple chaperones into organized, functional complexes and facilitate the "handoff" of clients between them. PPIs also link chaperones and their clients to other cellular pathways, such as those that mediate trafficking (e.g., cytoskeleton) and degradation (e.g., proteasome). The PPIs of the chaperone network have a wide range of affinity values (nanomolar to micromolar) and involve many distinct types of domain modules, such as J domains, zinc fingers, and tetratricopeptide repeats. Many of these motifs have the same binding surfaces on shared partners, such that members of one chaperone class often compete for the same interactions. Somehow, this collection of PPIs draws together chaperone families and creates multiprotein subnetworks that are able to make the "decisions" of protein quality control. The key to understanding chaperone-mediated proteostasis might be to understand how PPIs are regulated. This Account will discuss the efforts of our group and others to map, measure, and chemically perturb the PPIs within the molecular chaperone network. Structural biology methods, including X-ray crystallography, NMR spectroscopy, and electron microscopy, have all played important roles in visualizing the chaperone PPIs. Guided by these efforts and -omics approaches to measure PPIs, new advances in high-throughput chemical screening that are specially designed to account for the challenges of this system have emerged. Indeed, chemical biology has played a particularly important role in this effort, as molecules that either promote or inhibit specific PPIs have proven to be invaluable research probes in cells and animals. In addition, these molecules have provided leads for the potential treatment of protein misfolding diseases. One of the major products of this research field has been the identification of putative PPI drug targets within the chaperone network, which might be used to change chaperone "decisions" and rebalance proteostasis. [ABSTRACT FROM AUTHOR]

Readily functionalizable bipyrimidine compounds were prepared for the first time, and their coordination chemistry with silver salts was explored. Solution ¹H NMR spectroscopy experiments indicated that the ligands rapidly form complexes with silver(I) salts, and coordination at a first site inhibits coordination of a second cation to the ligand, thus favoring 1:1 complexes in solution. These 1:1 units self-assemble into one-dimensional chains in the solid state, even in the presence of excess Ag(I). Structurally diverse coordination polymers exhibiting different coordination numbers and geometry were characterized by single crystal X-ray crystallography. Our results demonstrate that a modification to the ligand, distal from the binding site, affects the coordination chemistry and supramolecular structure of these complexes. [ABSTRACT FROM AUTHOR]

Bacterial NO reductase (bacNOR) enzymes utilize a heme/non-heme active site to couple two NO molecules to N2O. We show that BF3 coordination to the nitrosyl O-atom in (OEP)Fe(NO) activates it toward N-N bond formation with NO to generate N2O. 15N-isotopic labeling reveals a reversible nitrosyl exchange reaction and follow-up N-O bond cleavage in the N2O formation step. Other Lewis acids (B(C6F5)3 and K+) also promote the NO coupling reaction with (OEP)Fe(NO). These results, complemented by DFT calculations, provide experimental support for the cis:b3 pathway in bacNOR. [ABSTRACT FROM AUTHOR]

The nature of actinide-actinide bonds has attracted considerable attention for a long time, especially since recent theoretical studies suggest that triple and up to quintuple bonds should be possible, but little is known experimentally. Actinide-actinide bonds inside fullerene cages have also been proposed, but their existence has been debated intensively by theoreticians. Despite all the theoretical arguments, critical experimental data for a dimetallic actinide endohedral fullerene have never been obtained. Herein, we report the synthesis and isolation of a dimetallic actinide endohedral metallofullerene (EMF), U2@C80. This compound was fully characterized by mass spectrometry, single crystal X-ray crystallography, UV-vis-NIR spectroscopy, Raman spectroscopy, cyclic voltammetry, and X-ray absorption spectroscopy (XAS). The single crystal X-ray crystallographic analysis unambiguously assigned the molecular structure to U2@Ih(7)-C80. In particular, the crystallographic data revealed that the U-U distance is within the range of 3.46- 3.79 Å, which is shorter than the 3.9 Å previously predicted for an elongated weak U-U bond inside the C80 cage. The XAS results reveal that the formal charge of the U atoms trapped inside the fullerene cage is +3, which agrees with the computational and crystallographic studies that assign a hexaanionic carbon cage, (Ih-C80)6-. Theoretical studies confirm the presence of a U-U bonding interaction and suggest that the weak U-U bond in U2@Ih(7)-C80 is strengthened upon reduction and weakened upon oxidation. The comprehensive characterization of U2@Ih(7)-C80 and the overall agreement between the experimental data and theoretical investigations provide experimental proof and deeper understanding for actinide metal-metal bonding interactions inside a fullerene cage. [ABSTRACT FROM AUTHOR]

Crystals of the heterocyclic radical naphtho- 1,3,2-dithiazolyl NDTA display magnetic bistability with a well-defined hysteretic phase transition at Tc↓ = 128(2) K and Tc↑ = 188(2) K. The magnetic signature arises from a radical/dimer interconversion involving one of the two independent π-radicals in the P1¯ unit cell. Variable temperature X-ray crystallography has established that while all the radicals in HT-NDTA serve as paramagnetic (S = 1/2) centers, half of the radicals in LT-NDTA form closed-shell N-N σ-bonded dimers (S = 0) and half retain their S = 1/2 spin state. The wide window of bistability (60 K) may be attributed to the large structural changes that accompany the phase transition. [ABSTRACT FROM AUTHOR]

Experimental charge density distribution studies, complemented by quantum mechanical theoretical calculations, of a host-guest system composed of a macrocycle (1) and barbital (2) in a 1:1 ratio (3) have been carried out via high-resolution single-crystal X-ray diffraction. The data were modeled using the conventional multipole model of electron density according to the Hansen-Coppens formalism. The asymmetric unit of macrocycle 1 contained an intraannular ethanol molecule and an extraannular acetonitrile molecule, and the asymmetric unit of 3 also contained an intraannular ethanol molecule. Visual comparison of the conformations of the macrocyclic ring shows the rotation by 180° of an amide bond attributed to competitive hydrogen bonding. It was found that the intraannular and extraannular molecules inside were orientated to maximize the number of hydrogen bonds present, with the presence of barbital in 3 resulting in the greatest stabilization. Hydrogen bonds ranging in strength from 4 to 70 kJ mol-1 were the main stabilizing force. Further analysis of the electrostatic potential among 1, 2, and 3 showed significant charge redistribution when cocrystallization occurred, which was further confirmed by a comparison of atomic charges. The findings presented herein introduce the possibility of high-resolution X-ray crystallography playing a more prominent role in the drug design process. [ABSTRACT FROM AUTHOR]

Tetraarylpyrrolo[3,2-b]pyrroles (TAPPs) possessing [1,1'-biphenyl]-2-yl substituents attached to the pyrrolic nitrogen atoms undergo selective double dehydrogenative cyclization accompanied by twofold 1,2-aryl migration under oxidative aromatic coupling conditions. The structure of the product of the rearrangement has been unambiguously confirmed by X-ray crystallography, and the reaction pathway is supported by density functional theory (DFT) calculations. Six-membered ring formation (requiring rearrangement of aryl substituents around the core) is energetically preferred over seven-membered ring closure, and a 1,2-aryl shift occurs via arenium cation intermediate. [ABSTRACT FROM AUTHOR]

A general and facile method to prepare unquaternized C-bound boron enolates by a ligandcontrolled O-to-C isomerization is reported. Using this protocol, C-bound pinacolboron enolates have been isolated in pure form for the first time, and have been fully characterized by NMR spectroscopy and X-ray crystallography. In contrast to the general perception, such C-boron enolates are stable without coordinative saturation at the boron. Moreover, C-boron enolates present reactivities that are distinct from the O-boron enolates, and their applications in C-O and C-C bond formations are demonstrated. [ABSTRACT FROM AUTHOR]

Fine tuning nanoparticles with atomic precision is exciting and challenging and is critical for tuning the properties, understanding the structure- property correlation and determining the practical applications of nanoparticles. Some ultrasmall thiolated metal nanoparticles (metal nanoclusters) have been shown to be precisely doped, and even the protecting staple metal atom could be precisely reduced. However, the precise addition or reduction of the kernel atom while the other metal atoms in the nanocluster remain the same has not been successful until now, to the best of our knowledge. Here, by carefully selecting the protecting ligand with adequate steric hindrance, we synthesized a novel nanocluster in which the kernel can be regarded as that formed by the addition of two silver atoms to both ends of the Pt@Ag12 icosohedral kernel of the Ag24Pt(SR)18 (SR: thiolate) nanocluster, as revealed by single crystal X-ray crystallography. Interestingly, compared with the previously reported Ag24Pt(SR)18 nanocluster, the as-obtained novel bimetal nanocluster exhibits a similar absorption but a different electrochemical gap. One possible explanation for this result is that the kernel tuning does not essentially change the electronic structure, but obviously influences the charge on the Pt@Ag12 kernel, as demonstrated by natural population analysis, thus possibly resulting in the large electrochemical gap difference between the two nanoclusters. This work not only provides a novel strategy to tune metal nanoclusters but also reveals that the kernel change does not necessarily alter the optical and electrochemical gaps in a uniform manner, which has important implications for the structure-property correlation of nanoparticles. [ABSTRACT FROM AUTHOR]

Simpterpenoid A (1), an unprecedented meroterpenoid possessing a highly functionalized cyclohexadiene moiety (ring C) featuring gem-propane-1,2-dione and methylformate groups, was characterized from mangrove-derived Penicillium simplicissimum MA-332. Due to the highly oxygenated and functionalized ring C and lack of some key correlations, the unambiguous assignment of the planar structure and steric configuration was solved by X-ray crystallographic analysis. Compound 1 exhibited inhibitory activity against influenza neuraminidase in nanomolar quantities. [ABSTRACT FROM AUTHOR]

A polycyclic imidazolophosphinine has been synthesized by collapse of the bridge of an appropriate 7-phosphanorbornene. This stable compound has been characterized by X-ray crystal structure analysis. It is fully planar with a P=C bond length of 1.733(4) Å. The lone pair at P is poorly reactive and corresponds to HOMO-3. The compound reacts with a protic acid and methyl iodide at the sp² nitrogen and with AuCl with the a-methoxy substituent, yielding a zwitterionicacylphosphidewhose complexation at P gives a bis-gold complex. Both the protonated product and the bis-gold complex have been characterized by X-ray crystal structure analysis. [ABSTRACT FROM AUTHOR]

The reaction of Cp*MCl3 (M = Zr, Zr1; M = Hf, Hf1) with the reducing agent Na/Hg (20% Na) and with sterically encumbered pentafulvenes adamantylidenepentafulvene AdFv, 6,6′-di-p-tolylpentafulvene pTol2Fv, and benzofulvenes adamantylidenebenzofulvene AdBzFv, 10,10′-di-p-tolylbenzofulvene pTol2BzFv, and 10,10′-diphenylbenzofulvene Ph2BzFv yielded the corresponding pentafulvene complexes (η5-pentamethylcyclopentadienyl)metal(η5:η¹-pentafulvene)chloride (Zr2a,b, Hf2a,b) and benzofulvene complexes (η5-pentamethylcyclopentadienyl)metal(η5:η¹-benzofulvene)chloride (Zr3a-c, Hf3a). This reductive complexation approach can be used in a multigram scale and mostly very good yields (up to 92%). In addition to NMR spectroscopic analyses, the pentafulvene complex Zr2b and benzofulvene complex Zr3b were characterized by X-ray crystallography, showing mainly the π-η5:σ-η¹ dianionic bonding mode together with slight influence of the π-η²:π-η³:σ-η¹ bonding mode. By use of the prochiral benzofulvenes the corresponding complexes Zr3a-c and Hf3a are furthermore obtained in a diastereoselective manner. [ABSTRACT FROM AUTHOR]

Pan assay interference compounds (PAINS) have become a paradigm for compound classes that might cause artifacts in biological assays. PAINS-defining substructures are typically contained in larger compounds. We have systematically examined X-ray structures of protein-ligand complexes for compounds containing PAINS motifs. In 2874 X-ray structures, 1107 unique ligands with PAINS substructures belonging to 70 different classes were identified. PAINS most frequently detected in crystallographic ligands included a number of prominent candidates such as quinones, catechols, or Mannich bases. However, on the basis of X-ray data, the presence of specific ligand-target interactions and reactivity under assay conditions were not mutually exclusive. In some instances, reactivity of ligands was likely responsible for complex formation. Different categories of PAINS-containing ligands were distinguished, which aided in the interpretation of specific interactions versus potential assay artifacts. Careful consideration of structural data adds another dimension to the analysis of interference compounds. [ABSTRACT FROM AUTHOR]

Human carbonic anhydrase IX (CA IX) is upregulated in neoplastic tissues; as such, it is studied as a drug target for anticancer chemotherapy. Inhibition of CA IX has been shown to be therapeutically favorable in terms of reducing tumor growth. Previously, saccharin, a commonly used artificial sweetener, has been observed to selectively inhibit CA IX over other CA isoforms. In this study, X-ray crystallography showed acesulfame potassium (Ace K) binding directly to the catalytic zinc in CA IX (mimic) and through a bridging water in CA II. This modulation in binding is reflected in the binding constants, with Ace K inhibiting CA IX but not other CA isoforms. Hence, this study establishes the potential of Ace K (an FDA approved food additive) as a lead compound in the design and development of CA IX specific inhibitors. [ABSTRACT FROM AUTHOR]

Phosphopantetheine adenylyltransferase (PPAT) is a rate-limiting enzyme essential for biosynthesis of coenzyme A (CoA), which in turn is responsible to regulate the secretion of exotoxins via type III secretion system in Pseudomonas aeruginosa, causing severe health concerns ranging from nosocomial infections to respiratory failure. Acetyl coenzyme A (AcCoA) is a newly reported inhibitor of PPAT, believed to regulate the cellular levels of CoA and thereby the pathogenesis. Very little is known so far regarding the mechanistic details of AcCoA binding inside PPAT-binding cleft. Herein, we have used extensive umbrella sampling simulations to decipher mechanistic insight into the inhibitor accommodation inside the binding cavity. We found that R90 and D94 residues act like a gate near the binding cavity to accommodate and stabilize the incoming ligand. Mutational models concerning these residues also show considerable difference in AcCoA-binding thermodynamics. To substantiate our findings, we have solved the first crystal structure of apo-PPAT from P. aeruginosa, which also found to agree with the simulation results. Collectively, these results describe the mechanistic details of accommodation of inhibitor molecule inside PPAT-binding cavity and also offer valuable insight into regulating cellular levels of CoA/AcCoA and thus controlling the pathogenicity. [ABSTRACT FROM AUTHOR]

Four isomeric propyl-bridged di(cyanate ester) monomers having an unexpectedly wide range of melting points were analyzed using X-ray crystallography, thermal analysis, and both empirical and semiempirical modeling, in order to examine the structure–property relationships that determine the melting characteristics. The four monomers’ crystal structures were determined, and intermolecular contacts and packing were examined. Enthalpies and entropies of melting were determined experimentally via differential scanning calorimetry and compared against two empirical models. Computational insights were provided by examining the monomers’ energetic rotational barriers. Significant effects that could not be accounted for within the framework of either the empirical or semiempirical models altered the entropy of melting over a range spanning about 40% of the average value, while the enthalpy of melting varied over a range equivalent to 50% of the average value. These large variations, even within an isomeric series exhibiting a high similarity in chemical structure, combined with an apparent correlation between the two parameters, complicate the prediction of melting phenomena for technologically important molecules, even when data for close structural analogues are available. [ABSTRACT FROM AUTHOR]

Antibiotic rifampicin was recrystallized from solutions containing aliphatic alcohols, ketones, or dimethyl sulfoxide. Thirteen new solvates were obtained that were studied by X-ray crystallography. In these solvates rifampicin exists in a zwitterionic form. The reported solvates are classified into eight different structural types. Whereas rifampicin molecules in the solvates form diverse assemblies via hydrogen bonds, the recurring structural motif in these crystals is generated by nonspecific intermolecular interactions. This motif has the form of a periodic one-dimensional (1D) rod, and similar 1D motifs were found in the structures of other zwitterionic or ionic rifamycins. In rifampicin solvates, these rods form a basis for the construction of two types of two-dimensional (2D) periodic modules: monolayers found in six structural types of rifampicin solvates and bilayers observed in two types of solvates. Diverse mutual arrangements of these 2D modules lead to the formation of channels with accommodated solvent molecules that consist of 10–40% of the crystal volume. Differential thermal analysis/thermogravimetric analyses and powder X-ray diffraction show that desolvation of the rifampicin 2-propanol solvate results in polymorph II of rifampicin. We show here that solvate decomposition may be a route to transformation of a thermodynamically stable polymorphic form into a metastable one. [ABSTRACT FROM AUTHOR]

Orychophragines A–C (1–3), three new alkaloids with an novel 2-piperazinone-fused 2,4-dioxohexahydro-1,3,5-triazine skeleton, were isolated from the seeds of Orychophragmus violaceus. Their structures were established on the basis of spectroscopic analysis and X-ray crystallographic analysis. Orychophragines A (1) exhibited remarkable cytotoxicity against HepG2, A549, Hela, and HCT-116 cells with IC50 values of 7.73, 10.79, 11.91, and 9.93 μM, respectively. Orychophragines C (3) showed moderate 60Co γ radiation protection activity in HUVEC cells. A plausible biosynthetic pathway for 1–3 was proposed [ABSTRACT FROM AUTHOR]

The irreversible transformation from an icosahe-dral quasicrystal (i-QC) CaAu[sub 439]Al[sub 161] to its cubic 2/1 crystalline approximant (CA) Ca[sub 13]Au[sub 56 31]([sub 3])Al[sub 2169] (CaAu[sub 433]([sub 1])Al[sub 167], Pa3 (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au[sub 59].[sub 86]([sub 2])Al[sub 17].[sub 14]0[sub 3].[sub 00]] and an icosahedral shell of only Al [Al[sub 105-15]]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au-Al nearest neighbor contacts over homoatomic Al-Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. According to electronic structure calculations, a cubic 1/1 CA, "Ca24Au[sub 88]Al64" (CaAu3.67Al2.67) is proposed. [ABSTRACT FROM AUTHOR]

De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn[sup 2+] and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn[sup 2+] clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn[sup 2+] and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix -- helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn[sup 2+] in an unanticipated geometry, and the fourth bound multiple Zn[sup 2+] at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures. [ABSTRACT FROM AUTHOR]

This study investigated the dynamic photo-response of pseudorotaxane crystals with azobenzene and ferrocenyl groups in the axle component. X-ray crystallography showed pseudorotaxanes with a methylazobenzene group and a dibromophenylene ring in the cyclic component to exhibit twisting of the trans-azobenzene groups at torsion angles of 17° and 38°, respectively. Repeated alternating laser irradiation of the crystals at 360 and 445 nm produced bending of 20-30° in opposite directions, with no evidence of decay. Under 445 nm irradiation, bending took place within 0.3 s. A crystal of nonsubstituted pseudorotaxane showed bending of only 2° under 360 nm irradiation due to multiple π-π interactions between the planar trans-azobenzene groups. The pseudorotaxane crystals have two chromophores, bent rapidly and reversibly on irradiation at rates depending on the molecular structure. [ABSTRACT FROM AUTHOR]

Herein, we report the discovery and characterization of a novel class of PAK4 inhibitors with a quinazoline scaffold. Based on the shape and chemical composition of the ATP-binding pocket of PAKs, we chose a 2,4-diaminoquinazoline series of inhibitors as a starting point. Guided by X-ray crystallography and a structure-based drug design (SBDD) approach, a series of novel 4-aminoquinazoline-2-carboxamide PAK4 inhibitors were designed and synthesized. The inhibitors' selectivity, therapeutic potency, and pharmaceutical properties were optimized. One of the best compounds, 31 (CZh226), showed remarkable PAK4 selectivity (346-fold vs PAK1) and favorable kinase selectivity profile. Moreover, this compound potently inhibited the migration and invasion of A549 tumor cells by regulating the PAK4-directed downstream signaling pathways in vitro. Taken together, these data support the further development of 31 as a lead compound for PAK4-targeted anticancer drug discovery and as a valuable research probe for the further biological investigation of group II PAKs. [ABSTRACT FROM AUTHOR]

[Pt(SiHPh2)2(dmpe)] (dmpe = 1,2-bis(dimethylphosphino)ethane) reacts with arylboronic acids to produce six-membered platinacycles [tiebar above startPt(SiPh2-O-BAr-O-tiebar above endSiPh2)(dmpe)] (Ar = C6H4-4-COMe (1a), C6H4-4-CF3 (1b)). X-ray crystallography of 1a revealed the structure having a planar six-membered ring, composed of Pt, O, B, and Si atoms. Reaction of H2O with [Pt(SiHPh2)2(dmpe)] formed a four-membered cyclic complex, [tiebar above startPt(SiPh2-O-Stiebar above endiPh2)(dmpe)] (2), which was observed in the initial reaction mixture of 4-acetylphenylboronic acid with [Pt(SiHPh2)2(dmpe)]. Exposure of solutions of [Pt(SiHPh2)2(dmpe)] and of [Pt(SiHAr2)2(PMe3)2] (Ar = Ph, C6H4-4-Me) to air resulted in the formation of the cyclic platina(siloxane)s, [tiebar above startPt(O-SiPh2-O-SiPh2tiebar above end-O)(dmpe)] (3) and [tiebar above startPt(O-SiAr2-O-SiAr2-tiebar above endO)(PMe3)2] (4: Ar = Ph; 5: Ar = C6H4-4-Me), respectively. The six-membered platina(borasiloxane) 1a reacts with H2GePh2 and with CF3CO2H to release the cyclic borasiloxanes as the products. The former reaction affords [Pt(GeHPh2)2(dmpe)], while the latter produces [Pt(OCOCF3)2(dmpe)] as the Pt-containing products. A similar reaction of HCl with platina(siloxane) 4 gives a disiloxanediol via cleavage of the Pt-O bonds. Complex 4 reacts with H2SiPh2 to form a triplatinum complex, [{Pt(PMe3)}3(μ-SiPh2)3] (15), which is obtained under milder conditions than the previously reported reaction starting from [Pt(SiHPh2)2(PMe3)2]. [ABSTRACT FROM AUTHOR]

Three sulfur-containing compounds, kujounins A1 (1) and A2 (2) and allium sulfoxide A1 (3), were isolated from the acetone extract of Allium fistulosum 'Kujou'. Their chemical structures were elucidated on the basis of physicochemical evidence, including X-ray crystallographic data. Compounds 1 and 2 possess three rings and an acetal structure and were obtained as complex compounds having disulfide and monosaccharide moieties. On the other hand, compound 3 has a thiolane skeleton derived from allicin. Naturally occurring compounds 1-3 have rare molecular skeletons. This study is the first to determine the absolute configuration of thiolane-type compounds. [ABSTRACT FROM AUTHOR]

SufU is a zinc-containing protein involved in mobilization of sulfur from SufS for iron-sulfur cluster biogenesis of Bacillus subtilis. Structural basis for the sulfur transfer in SufS-SufU complex was revealed. A zinc-ligand exchange reaction upon SufS-SufU complexation provides a free thiol from Cys41 of SufU as a sulfur acceptor. [ABSTRACT FROM AUTHOR]

Herein we report the optimization of a series of pyrrolopyrimidine inhibitors of interleukin-1 receptor associated kinase 4 (IRAK4) using X-ray crystal structures and structure based design to identify and optimize our scaffold. Compound 28 demonstrated a favorable physicochemical and kinase selectivity profile and was identified as a promising in vivo tool with which to explore the role of IRAK4 inhibition in the treatment of mutant MYD88L265P diffuse large B-cell lymphoma (DLBCL). Compound 28 was shown to be capable of demonstrating inhibition of NF-κB activation and growth of the ABC subtype of DLBCL cell lines in vitro at high concentrations but showed greater effects in combination with a BTK inhibitor at lower concentrations. In vivo, the combination of compound 28 and ibrutinib led to tumor regression in an ABC-DLBCL mouse model. [ABSTRACT FROM AUTHOR]

The NCN palladium(II) pincer complex [Benzoyl(N∧C∧N)PdBr] (16) was synthesized by the oxidative addition of Benzoyl(N∧C∧N)Br to Pd(dba)2 in 85% yield [(N∧C∧N) = 5-tert-butyl-1,3-bis(N-substituted benzimidazol-2'-yl)phenyl)]. Then treatment of complex 16 with KI yielded the iodopalladium complex [Benzoyl(N∧C∧N)PdI] (17) in 92% yield. Furthermore, a series of cationic palladium(II) complexes, including [Benzoyl(N∧C∧N)Pd(MeCN)]+[BF4]- (18), [Benzoyl(N∧C∧N)Pd(MeCN)]+[SbF6]- (19), and [Benzoyl(N∧C∧N)Pd(OTf)] (20), were prepared in 68-79% yields by the reaction of the neutral palladium(II) complex (16) with AgBF4, AgSbF6, and AgOTf, respectively. Similarly, previously synthesized Tosyl(N∧C∧N)PdBr [5-tert-butyl-1,3-bis(N-tosylbenzimidazol-2'-yl)phenyl]palladium bromide (5b) was treated with AgSO3CF3 and AgSbF6 to afford cationic palladium(II) complexes [Tosyl(N∧C∧N)Pd(OTf)] (21) and [Tosyl(N∧C∧N)Pd(MeCN)]+[SbF6]- (22) in 41 and 61% yields, respectively. 5-tert-Butyl-1,3-bis[{(N-tosylbenzimidazol-2'-yl)phenyl}palladium(II)] triflate (21) exhibited an unsupported metallophillic Pd•••Pd interaction [3.166(8) Å] that is corroborated by X-ray crystallographic studies. Compared to other cationic palladium complexes, complex 21 was found to be less stable. In Atoms in Molecule (AIM) analysis, the bond critical point (ρ) between Pd and Pd atoms is 0.000865 au, supporting the presence of metallophillic interaction in complex 21. The bond strength of the Pd•••Pd bond was also measured by density functional theory calculations that indicated that the calculated bond order was approximately one-fourth of the normal covalent Pd-Pd bond (natural atomic orbital bond order method). All eight complexes, two neutral and six cationic, were characterized by common spectroscopic techniques, and six complexes were corroborated by X-ray diffraction studies. [ABSTRACT FROM AUTHOR]

Amination of 2,2"-dibromo-p-terphenyl with 2,6-diisopropylaniline, through Pd mediated cross coupling, yields the p-terphenyl bis(aniline) ligand H2LAr. Deprotonation of H2LAr with excess KH generates the dianion [K(DME)2]2LAr as a dark red solid. Treatment of [K(DME)2]2LAr with UI3(dioxane)1.5 produces the mononuclear U(III) complex LArU(I)(DME) (1). Subsequent addition of the nucleophilic metal anion [CpFe(CO)2]- (Fp-) gives the bimetallic U(III) compound LArU(Fp) (2) in modest yield which features a rare instance of an unsupported U-M bond. Inspection of the metrical parameters of the solid-state structures of 1·DME and 2·0.5DME from X-ray crystallographic analyses show a seemingly η6-interaction between the uranium and the terphenyl ligand (1: U1-Ccentroid = 2.56 Å; 2: U1-Ccentroid = 2.45 Å), spatially imposed as a consequence of the anilide N-donor atom coordination. Furthermore, the U-Fe bond length in 2 (U1-Fe1 = 2.9462(3) Å) is consistent with a metal-metal single bond. Notably, electronic structure analyses by CASPT2 calculations instead suggest that electrostatic, and not covalent, interactions dominate between the U-arene systems in 1 and 2 and between the U-Fe bond in the latter. [ABSTRACT FROM AUTHOR]

The synthesis of a new family of iodonium zwitterions, in which the formal anion is a trifluoroborate moiety, is reported. These reagents present very good stability and have high resistance toward benzyne formation. Their structures were confirmed by X-ray crystallographic analysis and were further investigated using DFT calculations. QTAIM analysis supports an ionic, noncovalent, I+···BF3- interaction, in accordance with a true zwitterionic nature. Preliminary results of synthetic applications, the arylation of phenolates and trifluoroborate group functionalization, are reported. [ABSTRACT FROM AUTHOR]