Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole

For the structure of fluconazole [systematic name: 2‐(2,4‐difluorophenyl)‐1,3‐bis(1H‐1,2,4‐triazol‐1‐yl)propan‐2‐ol] monohydrate, C₁₃H₁₂F₂N₆O·H₂O, a case study on different model refinements is reported, based on single‐crystal X‐ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å⁻¹. The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical‐atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å⁻¹, but requires good low‐order data.     

Discovery of Novel PI3Kδ Inhibitors Based on the p110δ Crystal Structure

PI3Kδ is a key mediator of B-cell receptor signaling and plays an important role in the pathogenesis of certain hematological malignancies, such as chronic lymphocytic leukemia. Idelalisib, which targets PI3Kδ specifically, is the first approved PI3K inhibitor for cancer therapy. Recently, we carried out virtual screening, cell-based assays, adapta kinase assays, and molecular dynamic analysis to discover novel PI3Kδ inhibitors and identified NSC348884 as a lead PI3Kδ inhibitor. NSC348884 had an excellent docking score, potent PI3Kδ-inhibitory activity, antitumor effects on various cancer cell lines, and a favorable binding mode with the active site of PI3Kδ. Moreover, through the structural modification of NSC348884, we further discovered comp#1, which forms H-bonds with both Val828 and Lys779 in the ATP binding pocket of PI3Kδ, with a more favorable conformation binding to PI3Kδ. In addition, we found that N¹, N¹, N²-trimethyl-N²-((6-methyl-1H-benzo[d]imidazol-2-yl) methyl) ethane-1,2-diamine might be a potential scaffold structure. Thus, the result of this study provides a far more efficient approach for discovering novel inhibitors targeting PI3Kδ.     

Explaining Cu@Pt Bimetallic Nanoparticles Activity Based on NO Adsorption

Cu@Pt nanoparticles (NPs) are experimentally regarded as improved catalysts for NO_x storage/reduction, with higher activities and selectivities compared with pure Pt or Cu NPs, and with inverse Pt@Cu NPs. Here, a density functional theory-based study on such NP models with different sizes and shapes reveals that the observed enhanced stability of Cu@Pt compared with Pt@Cu NPs is due to energetic reasons. On both types of core@shell NPs, charge is transferred from Cu to Pt, strengthening the NP cohesion energy in Pt@Cu NPs, and spreading charge along the surface in Cu@Pt NPs. The negative surface Pt atoms in the latter diminish the NO bonding owing to an energetic rise of the Pt bands, as detected by the appliance of the d-band model, although other factors, such as atomic low coordination or the presence of an immediate subsurface Pt atom do as well. A charge density difference analysis discloses a donation/back-donation mechanism in the NO adsorption.     

Unravelling the effect of the E545K mutation on PI3Kα kinase

PI3Kα controls several cellular processes and its aberrant signalling is implicated in tumorigenesis. One of its hotspot mutations, E545K, increases PI3Kα lipid kinase activity, but its mode of action is only partially understood. Here, we perform biased and unbiased molecular dynamics simulations of PI3Kα and uncover, for the first time, the free energy landscape of the E545K PI3Kα mutant. We reveal the mechanism by which E545K leads to PI3Kα activation in atomic-level detail, which is considerably more complex than previously thought.

The mechanism by which the cancer-causing E545K mutation may lead to PI3Kα activation is described in atomic-level detail.     

[Cu4Cl4(C10H16S4)2]的合成和晶体结构

早有文献[1]报导，二硫代乙酸丙酮C5H8S2(记为SacSac）能以下列三种形式存在于金属配合物中：（I）（SacSac）2M，如M=Ni，Co等，其中SacSac呈负一价，通过两个S原子和金属直接螫合；（11）（SacSaChMCI。；如M二Mn，CdSn等，（S。Sac）呈正一价，且以阳离子状态存在干晶体和溶     

Development of New Thiophene-Containing Triaryl Pyrazoline Derivatives as PI3Kγ Inhibitors

A series of new thiophene-containing triaryl pyrazoline derivatives, 3a–3t, were synthesized and evaluated regarding PI3K inhibition activity and anti-tumor potency based on a trial of introducing significant moieties, including pyrazoline and thiophene, and simplifying the parallel ring structures. Most of the tested compounds indicated potent PI3K inhibitory potency, with this series of compounds showing more potency for PI3Kγ than PI3Kα. The top hit 3s seemed more potent than the positive control LY294002 on inhibiting PI3Kγ (IC₅₀ values: 0.066 μM versus 0.777 μM) and more selective from PI3Kα (Index values: 645 versus 1.74). It could be inferred that the combination of para- and meta-, as well as the modification of the electron-donating moieties, led to the improvement in potency. The anti-proliferation inhibitory activity and the enzymatic inhibition potency indicated consistent tendencies. The top hit 3s could inhibit the phosphorylation of Akt by inhibiting PI3K through the PI3K-Akt-mTOR pathway. The molecular docking simulation indicated that the binding pattern of 3s into PI3Kγ was preferable than that of PI3Kα, with more hydrogen bond, more π-involved interactions, and fewer π-sulfur interactions. The information in this work is referable for the further development of selective inhibitors for specific isoforms of PI3K.     

Potential active sites of Mo single atoms for electrocatalytic reduction of N2

Single atom catalysts(SACs) with isolated metal atoms dispersed on supports exhibit distinctive performances for electrocatalysis reactions.The designable realization of well-dispersed single metal atoms is still a great challenge owing to their ease of aggregation.Here,Mo single atomic sites(Mo-N₃C)combined with some ultrasmall Mo₂C/MoN clusters(Mo-SA/Mo₂C-MoN-Cs,mean diameter <2 nm) on nitrogen-doped porous carbon were synthesized via a simple pyrolysis of bimetallic Zn/Mo metalorganic frameworks.X-ray absorption near edge spectra(XANES) in combination with various characterizations show that most of Mo species in sample exist in the form of single sites and the exact structure is Mo-N₃C.Density functional theory(DFT) calculation further shows that as the number of Ncoordination in the Mo-NxC moieties increases,the positive cha rge of Mo atoms increases.The single Mo atoms in Mo-N₃C have the best capability of N₂ adsorption,which may serve as main active sites for further electrochemical N2 reduction.     

Borylated 2,3,4,5-Tetrachlorophthalimide and Their 2,3,4,5-Tetrachlorobenzamide Analogues: Synthesis,Their Glycosidase Inhibition and Anticancer Properties in View to Boron Neutron Capture Therapy

Tetrachlorinated phthalimide analogues bearing a boron-pinacolate ester group were synthesised via two synthetic routes and evaluated in their glycosidase modulating and anticancer properties, with a view to use them in boron neutron capture therapy (BNCT), a promising radiation type for cancer, as this therapy does little damage to biological tissue. An unexpected decarbonylation/decarboxylation to five 2,3,4,5-tetrachlorobenzamides was observed and confirmed by X-ray crystallography studies, thus, giving access to a family of borylated 2,3,4,5-tetrachlorobenzamides. Biological evaluation showed the benzamide drugs to possess good to weak potencies (74.7–870 μM) in the inhibition of glycosidases, and to have good to moderate selectivity in the inhibition of a panel of 18 glycosidases. Furthermore, in the inhibition of selected glycosidases, there is a core subset of three animal glycosidases, which is always inhibited (rat intestinal maltase α-glucosidase, bovine liver β-glucosidase and β-galactosidase). This could indicate the involvement of the boron atom in the binding. These glycosidases are targeted for the management of diabetes, viral infections (via a broad-spectrum approach) and lysosomal storage disorders. Assays against cancer cell lines revealed potency in growth inhibition for three molecules, and selectivity for one of these molecules, with the growth of the normal cell line MCF10A not being affected by this compound. One of these molecules showed both potency and selectivity; thus, it is a candidate for further study in this area. This paper provides numerous novel aspects, including expedited access to borylated 2,3,4,5-tetrachlorophthalimides and to 2,3,4,5-tetrachlorobenzamides. The latter constitutes a novel family of glycosidase modulating drugs. Furthermore, a greener synthetic access to such structures is described.     

Synthesis,crystal structure,and electronic structure of a copper(II) chloride complex with 9(E)-phenanthrene-9,10-dione[(1Z)-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]hydrazone [Cu2(L-H)2Cl2]

The [Cu₂(L-H)₂Cl₂] compound (I) has been obtained by the reaction of 9(E)-phenanthrene-9,10-dione[(1Z)-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]hydrazone with copper(II) chloride. The crystal and molecular structure of I has been determined by X-ray crystallography. The L-H anion acts as a tridentate chelating ligand and is coordinated to the Cu atom through the O(1) atoms of the phenanthrenequinone moiety, the N(1) atom of the dihydroisoquinoline moiety, and the N(3) atom of the azo group to form two five-membered chelate rings. Complex I is a dimer with a double chloride bridge. The coordination polyhedron of the Cu atom is completed to a distorted pyramid by two chlorine atoms. The molecular and electronic structures of the L molecule and the model [Cu(L-H)Cl] complex have been determined by the density functional theory method. Spectroscopic characteristics of I have been determined.     

N-phenyl-6-chloro-4-hydroxy-2-quinolone-3-carboxamides: Molecular Docking,Synthesis, and Biological Investigation as Anticancer Agents

Cancer is a multifactorial disease and the second leading cause of death worldwide. Diverse factors induce carcinogenesis, such as diet, smoking, radiation, and genetic defects. The phosphatidylinositol 3-kinase (PI3Kα) has emerged as an attractive target for anticancer drug design. Eighteen derivatives of N-phenyl-6-chloro-4-hydroxy-2-quinolone-3-carboxamide were synthesized and characterized using FT-IR, NMR (¹H and ¹³C), and high-resolution mass spectra (HRMS). The series exhibited distinct antiproliferative activity (IC₅₀ µM) against human epithelial colorectal adenocarcinoma (Caco-2) and colon carcinoma (HCT-116) cell lines, respectively: compounds 16 (37.4, 8.9 µM), 18 (50.9, 3.3 µM), 19 (17.0, 5.3 µM), and 21 (18.9, 4.9 µM). The induced-fit docking (IFD) studies against PI3Kαs showed that the derivatives occupy the PI3Kα binding site and engage with key binding residues.     

Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations

We performed geometry optimizations using the tuned and balanced redistributed charge algorithms to treat the QM-MM boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. In the tuned and balanced redistributed charge (TBRC) scheme, the QM boundary atom is terminated by a tuned F link atom, and the charge of the MM boundary atom is properly adjusted to conserve the total charge of the entire QM/MM system; then the adjusted MM boundary charge is moved evenly to the midpoints of the bonds between the MM boundary atom and its neighboring MM atoms. In the tuned and balanced redistributed charge-2 (TBRC2) scheme, the adjusted MM boundary charge is moved evenly to all MM atoms that are attached to the MM boundary atom. A new option, namely charge smearing, has been added to the TBRC scheme, yielding the tuned and balanced smeared redistributed charge (TBSRC) scheme. In the new scheme, the redistributed charges near the QM-MM boundary are smeared to make the electrostatic interactions between the QM region and the redistributed charges more realistic. The TBRC2 scheme and new TBSRC scheme have been tested for various kinds of bonds at a QM-MM boundary, including C-C, C-N, C-O, O-C, N-C, C-S, S-S, S-C, C-Si, and O-N bonds. Charge smearing is necessary if the redistributed charges are close to the QM region, as in the TBSRC scheme, but not if the redistributed charge is farther from the QM region, as in the TBRC2 scheme. We found that QM/MM results using either the TBRC2 scheme or the TBSRC scheme agree well with full QM results; the mean unsigned error (MUE) of the QM/MM deprotonation energy is 1.6 kcal/mol in both cases, and the MUE of QM/MM optimized bond lengths over the three bonds closest to the QM-MM boundary, with errors averaged over the protonated forms and unprotonated forms, is 0.015 ? for TBRC2 and 0.021 ? for TBSRC. The improvements in the new scheme are essential for QM-MM boundaries that pass through a polar bond, but even for boundaries that pass through C-C bonds, the improvement can be quite significant.     

Neutron elastic scattering studies of biological molecules and complexes

Neutron diffraction can provide very precise stereochemical information about hydrogen bonds and other features involving hydrogen atoms in crystals. This is because, unlike for x rays, the hydrogen atom has a significant scattering amplitude for neutrons relative to other atoms. High-precision studies of a class of molecules, like those on α-amino acids carried out at Brookhaven and Trombay, can provide important information on systematics of the structure, conformation, and hydrogen bonding parameters. Some attempts have also been made to extend these single-crystal studies to some proteins like myoglobin, lysozyme, and trypsin. The large anomalous scattering amplitudes for some stable isotopes like ¹¹³Cd and ¹⁴⁹Sm and the easy variability of neutron wavelength also provides, in principle, a method for solving the phase problem without crystallizing too many heavy atom derivatives. The combination of neutron and x-ray diffraction data, now being used to study charge density distributions in organic molecules and hydrogen bonds, may be extended in the future to larger molecules of biological importance. The small-angle scattering of neutrons is also a powerful technique for studying large biological particles in solution at low resolution to obtain information about sizes, shapes and distribution of constituents.     

Piezo-Responsive Hydrogen-Bonded Frameworks Based on Vanillin-Barbiturate Conjugates

A concept of piezo-responsive hydrogen-bonded π-π-stacked organic frameworks made from Knoevenagel-condensed vanillin–barbiturate conjugates was proposed. Replacement of the substituent at the ether oxygen atom of the vanillin moiety from methyl (compound 3a) to ethyl (compound 3b) changed the appearance of the products from rigid rods to porous structures according to optical microscopy and scanning electron microscopy (SEM), and led to a decrease in the degree of crystallinity of corresponding powders according to X-ray diffractometry (XRD). Quantum chemical calculations of possible dimer models of vanillin–barbiturate conjugates using density functional theory (DFT) revealed that π-π stacking between aryl rings of the vanillin moiety stabilized the dimer to a greater extent than hydrogen bonding between carbonyl oxygen atoms and amide hydrogen atoms. According to piezoresponse force microscopy (PFM), there was a notable decrease in the vertical piezo-coefficient upon transition from rigid rods of compound 3a to irregular-shaped aggregates of compound 3b (average values of d₃₃ coefficient corresponded to 2.74 ± 0.54 pm/V and 0.57 ± 0.11 pm/V), which is comparable to that of lithium niobate (d₃₃ coefficient was 7 pm/V).     

Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction

Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs.     

Cu4Mo6Se8: synthesis, crystal structure, and electronic structure of a new Chevrel phase structure type

Cu4Mo6Se8 has been synthesized by intercalation of Cu into Cu2Mo6Se8 at room temperature, and its crystal structure has been determined. This compound crystallizes in the triclinic space group P, with a = 6.7609(8) A, b = 6.8122(7) A, c = 7.9355(10) A, alpha = 70.739(4) degrees , beta = 72.669(4) degrees , gamma = 84.555(5) degrees , and Z = 1. Instead of residing in the voids between corners or edges of Mo6Se8 clusters as in the classic R Chevrel structure, the Cu atoms in Cu4Mo6Se8 fully occupy four sites between faces of two adjacent Mo6Se8 clusters. Thus, two of the six Mo atoms in each cluster do not have capping Se atoms from neighboring clusters. This represents a new triclinic structure type for Chevrel phases. In addition to the synthesis and crystal structure, we present and discuss results from electronic structure calculations using both extended Hückel and density functional theory. These calculations predict Cu4Mo6Se8 to be metallic. We also report results from Cu intercalation into Chevrel phase sulfides and tellurides. Preliminary experiments suggest that a telluride analogue of Cu4Mo6Se8 exists.     

True nanocable assemblies with insulating BN nanotube sheaths and conducting Cu nanowire cores

Nanocable models comprised of BN nanotubes filled with close-packed Cu nanowires were investigated by gradient-corrected density functional theory (DFT) computations. The optimal distance between the sidewall of BN nanotubes and the atoms in a copper nanowire is about 0.35 nm, with a weak insertion energy (ca. -0.04 eV per Cu atom). Hence, such nanocables are assembled by weaker van der Waals (vdW) forces, rather than by chemical bonding interactions. The electronic band structures of the BN/Cu hybrid systems are superposition of those of the separate components, the BN nanotubes, and the Cu nanowires. Since charge density analyses show that the conduction electrons are distributed only on the copper atoms, charge transport will occur only in these inner nanowires, which are effectively insulated by the outer BN nanotubes. On the basis of these computational results, BN/Cu hybrid structures should be ideal nanocables.     

Experimental electron density study of a complex between copper(II) and the antibacterial quinolone family member ciprofloxacin

An experimental charge density study of a 1 : 1 complex of Cu-cfx (cfx = ciprofloxacin), 1 [Cu(cfx)(H(2)O)(3)]SO4.2H(2)O, has been performed using single-crystal X-ray diffraction data collected at 100 K using conventional Mo Kalpha radiation. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the electron density with the atoms in molecules (AIM) approach. The copper atom binds to two oxygen atoms in one end of the zwitterionic form of the cfx molecule, in addition to forming bonds with three water molecules, forming a square pyramidal coordination geometry. AIM decomposition of the experimental electron density establishes that the copper atom binds more strongly to the cfx molecule than to the water molecules, suggesting that the latter can be detached leaving behind a reactive, water-free Cu-cfx complex available for interaction with e.g. a macromolecular site. AIM analysis of the extensive hydrogen bond pattern reveals that the positively charged N-end of the zwitterionic cfx forms a relatively strong N-H-O hydrogen bond implying that this region of cfx may play an important role in the docking process in the active site. Visualisation and statistics of selected density derived properties on the molecular surface of the isolated cfx molecule vs its metal complexed counterpart points out regions of potential reactivity. The effect of the fluorine atom is to expand the negative region of the electrostatic potential, while the nitrogen end is heavily electropositive and willingly donates to--for molecular docking purposes--relatively strong hydrogen bonding. The Cu atom is highlighted as a potentially highly reactive site which is likely to interact strongly with any given negative ligand.     

A series of novel Mo(W)/Cu/S heterobimetallic clusters containing SBu(t-) linkages. Synthesis, structure and spectroscopic characterisation

Six new copper(I) clusters, [Et4N]2[(MOS3)2Cu4(mu-SBu(t))2](1a: M = Mo; 1b: M = W), [Et4N][(MOS3)2Cu6(mu-SBu(t))3](2a: M = Mo; 2b: M = W) and [Bu4N]2[(MOS3)3Cu9(mu-SBu(t))3(mu3-SBu(t))][I](3a: M = Mo; 3b: M = W) have been prepared by the reactions of thiomolybdates and thiotungstates with CuSBu(t) under various conditions. The [(MOS3)2Cu4(mu-SBu(t))2](2-) dianions in 1a and 1b represent the first examples of double butterfly-shaped Mo(W)/Cu/S clusters. Addition of more Cu atoms to 1a or 1b resulted in the formation of incomplete double cubane-like clusters 2a or 2b. Single crystal structural studies showed that the anions of 2a and 2b are formed in a mouth-to-mouth fashion by two incomplete cubanes [MOS3Cu3](M = Mo, W) with three mu-SBu(t-) linkages. In the molecular structure of 3b, the SBu(t-) ligands act as mu- and mu3-bridges which link three WOS3Cu3 incomplete cubane-like fragments. An iodide ion crystallises in the cavity defined by the three incomplete cubanes in 3b. The spectroscopic and electrochemical properties of all the clusters are also studied.     

SYNTHESIS AND STRUCTURAL CHARACTERIZATION OF IN-COMPLETE CUBANE CLUSTER C(MoCu_3S_3) (O)(μ-dtp)(PPh_3)_3]

<正> A new mixed-metal sulfido incomplete cubane cluster [(MoCuS3) (O) (μ-dtp) (PPh3)3] Cdtp = S2P (OC2H5)2] has been prepared by reaction of (NH4)2MoOS3 with Cu(dtp) (PPh3)2 in dimethylformamide solution. It crystallizes in the triclinic space group P1, a = 13.810(5), b = 19. 753(5), c=11. 719(4) A. α=99. 42(2), β=107. 24(3),γ=88. 05(3)°, V = 3012(2)A3, Dc = l. 51g/cm3and Z = 2. Final R=0. 046, Rw = 0. 056 for 7700 unique intensity data(I≥3σ(I)). The central unit [MoCu3S3]3+ can be described as a distorted incomplete cube with one missing corner. The Mo atom is tetrahedrally coordinated by three μ3-S atoms and one terminal O atom. Two Cu atoms are tetrahedrally coordinated whereas the third Cu atom has a highly distorted trigonal environment. The mean Mo - Cu bond length is 2. 752A. The Cu...Cu distances are in the range of 3. 200(1) -3. 740(1) A which are too long to form bonds.     

The Effects of Chemical Bonding at Subatomic Resolution: A Case Study on α-Boron

Similar to classical asphericity shifts, aspherical deformations of the electron density in the atomic core region can result in core asphericity shifts in refinements using a Hansen-Coppens multipolar model (HCM), especially when highly precise experimental datasets with resolutions far beyond sin(θ)/λ ≤ 1.0 Å⁻¹ are employed. These shifts are about two orders of magnitude smaller than their counterparts caused by valence shell deformations, and their underlying deformations are mainly of dipolar character for 1st row atoms. Here, we analyze the resolution dependence of core asphericity shifts in α-boron. Based on theoretical structure factors, an appropriate Extended HCM (EHCM) is developed, which is tested against experimental high-resolution (sin(θ)/λ ≤ 1.6 Å⁻¹) single-crystal diffraction data. Bond length deviations due to core asphericity shifts of α-boron in the order of 4–6·10⁻⁴ Å are small but significant at this resolution and can be effectively compensated by an EHCM, although the correlation of the additional model parameters with positional parameters prevented a free refinement of all core model parameters. For high quality, high resolution data, a proper treatment with an EHCM or other equivalent methods is therefore highly recommended.