Comparison of covalency in the complexes of trivalent actinide and lanthanide cations

The complexes of trivalent actinide (Am(III) and Cm(III)) and lanthanide (Nd(III) and Sm(III)) cations with bis(2,4,4-trimethylpentyl)phosphinic acid, bis(2,4,4-trimethylpentyl)monothiophosphinic acid, and bis(2,4,4-trimethylpentyl)dithiophosphinic acid in n-dodecane have been studied by visible absorption spectroscopy and X-ray absorption fine structure (XAFS) measurements in order to understand the chemical interactions responsible for the great selectivity the dithiophosphinate ligand exhibits for trivalent actinide cations in liquid-liquid extraction. Under the conditions studied, each type of ligand displays a different coordination mode with trivalent f-element cations. The phosphinate ligand coordinates as hydrogen-bonded dimers, forming M(HL2)3. Both the oxygen and the sulfur donor of the monothiophosphinate ligand can bind the cations, affording both bidentate and monodentate ligands. The dithiophosphinate ligand forms neutral bidentate complexes, ML3, with no discernible nitrate or water molecules in the inner coordination sphere. Comparison of the Cm(III), Nd(III), and Sm(III) XAFS shows that the structure and metal-donor atom bond distances are indistinguishable within experimental error for similarly sized trivalent lanthanide and actinide cations, despite the selectivity of bis(2,4,4-trimethylpentyl)dithiophosphinic acid for trivalent actinide cations over trivalent lanthanide cations.     

Thermodynamic study of the complexation of trivalent actinide and lanthanide cations by ADPTZ, a tridentate N-donor ligand

To better understand the bonding in complexes of f-elements by polydentate N-donor ligands, the complexation of americium(III) and lanthanide(III) cations by 2-amino-4,6-di-(pyridin-2-yl)-1,3,5-triazine (ADPTZ) was studied using a thermodynamic approach. The stability constants of the 1:1 complexes in a methanol/water mixture (75/25 vol %) were determined by UV-visible spectrophotometry for every lanthanide(III) ion (except promethium), and yttrium(III) and americium(III) cations. The thermodynamic parameters (DeltaH degrees , DeltaS degrees) of complexation were determined from the temperature dependence of the stability constants and by microcalorimetry. The trends of the variations of DeltaG degrees , DeltaH degrees , and DeltaS degrees across the lanthanide series are compared with published results for other tridentate ligands and confirm strongly ionic bonding in the lanthanide-ADPTZ complexes. Comparison of the thermodynamic properties between the Am- and Ln-ADPTZ complexes highlights an increase in stability of the complexes by a factor of 20 in favor of the americium cation. This difference arises from a more exothermic reaction enthalpy in the case of Am, which is correlated with a greater degree of covalency in the americium-nitrogen bonds. Quantum chemistry calculations performed on a series of trivalent actinide and lanthanide-ADPTZ complexes support the experimental results, showing a slightly greater covalence in the actinide-ligand bonds that originates from a charge transfer from the ligand sigma orbitals to the 5f and 6d orbitals of the actinide ion.     

Mixed implicit/explicit solvation models in quantum mechanical calculations of binding enthalpy for protein–ligand complexes

An approach to quantum mechanical investigation of interactions in protein–ligand complexes has been developed that treats the solvation effect in a mixed scheme combining implicit and explicit solvent models. In this approach, the first solvation shell of the solvent around the solute is modeled with a limited number of hydrogen bonded explicit solvent molecules. The influence of the remaining bulk solvent is treated as a surrounding continuum in the conductor‐like screening model (COSMO). The enthalpy term of the binding free energy for the protein–ligand complexes was calculated using the semiempirical PM3 method implemented in the MOPAC package, applied to a trimmed model of the protein–ligand complex constructed with special rules. The dependence of the accuracy of binding enthalpy calculations on size of the trimmed model and number of optimized parameters was evaluated. Testing of the approach was performed for 12 complexes of different ligands with trypsin, thrombin, and ribonuclease with experimentally known binding enthalpies. The root‐mean‐square deviation (RMSD) of the calculated binding enthalpies from experimental data was found as ～1 kcal/mol over a large range. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Solution and structural investigations of ligand preorganization in trivalent lanthanide complexes of bicyclic malonamides

This report describes an investigation into the coordination chemistry of trivalent lanthanides in solution and the solid state with acyclic and preorganized bicyclic malonamide ligands. Two experimental investigations were performed: solution binding affinities were determined through single-phase spectrophotometric titrations and the extent of conformational change upon binding was investigated with single-crystal X-ray crystallography. Both experimental methods compare the bicyclic malonamide (BMA), which is designed to be preorganized for binding trivalent lanthanides, to an analogous acyclic malonamide. Results from the spectrophotometric titrations indicate that BMA exhibits a 10-100x increase in binding affinity to Ln(III) over acyclic malonamide. In addition, BMA forms compounds with high ligand-metal ratios, even when competing with water and nitrate ligands for binding sites. The crystal structures exhibit no significant differences in the nature of the binding between Ln(III) and the BMA or acyclic malonamide. These results support the conclusion that rational ligand design can lead to compounds that enhance the binding affinities within a ligand class.     

Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations

We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10. The results of the COMBINE analysis are compared with previously reported data obtained for the same dataset from modelled complexes that were based on an experimentally determined structure of the DhlA-dichloroethane complex. The quality of fit and the internal predictive power of the two COMBINE models are comparable, but better external predictions are obtained with the new approach. Both models show a similar composition of the principal components. Small differences in the relative contributions that are assigned to important residues for explaining binding affinity differences can be directly linked to structural differences in the modelled enzyme-substrate complexes: (i) rotation of all substrates in the active site about their longitudinal axis, (ii) repositioning of the ring of epihalohydrines and the halogen substituents of 1,2-dihalopropanes, and (iii) altered conformation of the long-chain molecules (halobutanes and halohexanes). For external validation, both a novel substrate not included in the training series and two different mutant proteins were used. The results obtained can be useful in the future to guide the rational engineering of substrate specificity in DhlA and other related enzymes.     

Synthesis, mesomorphism, and unusual magnetic behaviour of lanthanide complexes with perfluorinated counterions

Lanthanide complexes of the Schiff base ligand 4-dodecyloxy-N-hexadecyl-2-hydroxybenzaldimine and with perfluorinated alkyl sulfate counterions were synthesised. All of the metal complexes show a smectic A mesophase. The viscosity of this mesophase is much lower than that of analogous compounds with nitrate or alkyl sulfate counterions. The behaviour of these new highly anisotropic molecular magnetic materials was studied using high-temperature X-ray measurements in an external magnetic field and temperature-dependent magnetic susceptibility measurements. The mu(eff)-versus-temperature curve is more comparable with those expected for nematic phases than for smectic phases. The luminescence spectrum of a EuIII compound shows that the values of the second rank crystal field parameters are very large. The huge magnetic anisotropy can be related to this strong crystal-field perturbation.     

Molecular structure of Hf(BH4)4 investigated by quantum mechanical calculations and gas-phase electron diffraction

The structure of the gaseous hafnium tetrakis(tetrahydroborate) molecule, Hf(BH4)4, has been investigated by detailed quantum mechanical calculations and by analysis of its gas electron-diffraction (GED) pattern. The ground-state geometry possesses T symmetry with all of the triply-bridged BH4 groups twisted equally about the Hf...B-H axes. Salient structural parameters (ra distances, r angles) deduced from the GED pattern by the SARACEN method were: r(Hf...B) 231.4(2), r(Hf-Hb) 221.5(7), r(B-Hb) 127.6(5), r(B-Ht) 121(1) pm, Hf...B-Hb 69.4(3), Hb-B-Hb 108.4(4), Hb-B-Ht 110.6(3), B...Hf...B-Hb 166(1) degrees. A notable feature is the large magnitude of the Hf...B and Hf-Hb anharmonicity parameters, attributed to the fluxional hydrogen atom exchange process. The properties are compared with those of related tetrahydroborates..     

Conformational composition of cyclopentadienylphosphine investigated by microwave spectroscopy and quantum chemical calculations

The properties of cyclopentadienylphosphine have been investigated by means of Stark-modulation microwave spectroscopy and quantum chemical calculations at the MP2/aug-cc-pVTZ, B3LYP/6-311++G(d,p), and G3 levels of theory. Spectra attributable to two rotamers denoted conformers I and II have been assigned. Conformer I has a symmetry plane (Cs symmetry) consisting of the bisectors of the cyclopentadiene ring and of the phosphino group with the lone electron pair of phosphorus pointing toward the carbon ring. In conformer II, the phosphino group is rotated approximately 120 degrees out of this plane. Relative intensity measurements have been made, and it was found that conformer II is more stable than I by 1.3(4) kJ/mol. The preferred conformer represents a borderline case of intramolecular hydrogen bond stabilization. The experimental and MP2/ aug-cc-pVTZ rotational constants differ by several percent, which indicates that the aug-cc-pVTZ basis set is not large enough to be able to predict an accurate structure for the two conformers that are close to the equilibrium geometries. 5-Substituted 1,3-cyclopentadienyl derivatives may undergo circumambulatory rearrangements. However, there is no manifestation of this effect in the microwave spectrum of cyclopentadienylphosphine.     

Syntheses and luminescence of three lanthanide complexes constructed by flexible carboxylate ligand

Three new complexes, namely {[Ln(L)₃(2,2′-Bipy)] _n · H₂O} (Ln = Pr (I), Sm (II), and Nd (III)) (HL = 3-(2-hydroxyphenyl)propanoic acid), have been synthesized and structurally characterized. The structural determinations indicated (CIF files CCDC nos. 1472729 (I), 1472730 (II), 1472734 (III)) that I–III have similar dinuclear structures, which can be further linked into 2D sheet via the hydrogen bond interactions. Furthermore, the luminescent properties of I–III show the strong emissive power and feature.     

A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Kinetic isotope effect in the protonation of anthracenide salts by MeOH and MeOD role of counterions and solvents

Kinetics of protonation of Li⁺, Na⁺, K⁺, and Cs⁺ salts of anthracene radical anions (A^?_·,Cat⁺) and dianions (A^2?, 2Cat⁺) by MeOH and MeOD in tetrahydrofuran (THF) and dimethoxyethane (DME) led to the determination of the isotope effect (k_H/k_D) in the following reactions: Studies of cation and solvent influence on the rate constants of these reactions and on the magnitude of the isotope effect permitted us to draw some conclusions about the structure of the pertinent transition states. It seems that only the tight A^?·,Na⁺ pairs participate in the protonation, and on this basis the fraction of tight ion paris of A^?·,Na⁺ in DME was estimated. Our results have been compared with data reported in the literature.     

Terphenyl ligand systems in lanthanide chemistry: use of the 2,6-di(1-naphthyl)phenyl ligand for the synthesis of kinetically stabilized complexes of trivalent ytterbium, thulium, and yttrium

The molecular structures of terphenyl derivatives of trivalent ytterbium, thulium, and yttrium of general composition DnpLnCl(2)(THF)(2) [Dnp = 2,6-di(1-naphthyl)phenyl] are reported. The complexes (Ln = Yb: 1; Ln = Tm: 2; Ln = Y: 3) are synthesized by reaction of 1 equiv of DnpLi with 1 equiv of LnCl(3) (Ln = Yb, Tm, or Y) in tetrahydrofuran at room temperature in 50% yield. Attempts to prepare a Dnp scandium compound gave heterobimetallic [(THF)(3)Sc(2)OCl(5)Li(THF)](2) (4) in low yield. 1 crystallizes in the monoclinic space group C2/c. Crystal data for 1 at 203 K: a = 14.333(3) A, b = 16.353(3) A, c = 12.427(2) A, beta = 91.021(4) degrees, Z = 4, D(calcd) = 1.637 g cm(-3), R(1) = 4.44%. 2 crystallizes in the monoclinic space group C2/c. Crystal data for 2 at 203 K: a = 14.333(1) A, b = 16.374(2) A, c = 12.404(1) A, beta = 90.934(2) degrees, Z = 4, D(calcd) = 1.628 g cm(-3), R(1) = 3.00%. 3 crystallizes in the monoclinic space group C2/c. Crystal data for 3 at 203 K: a = 14.348(3) A, b = 16.476(3) A, c = 12.356(2) A, beta = 90.987(4) degrees, Z = 4, D(calcd) = 1.441 g cm(-3), R(1) = 5.62%. 4 crystallizes in the monoclinic space group P2(1)/n. Crystal data for 4 at 203 K: a = 11.0975(9) A, b = 11.0976(9) A, c = 21.3305(18) A, beta = 94.718(2) degrees, Z = 2, D(calcd) = 1.051 g cm(-3), R(1) = 3.45%. Complexes 1-3 represent examples of novel chiral (racemic) organometallic complexes of the lanthanide elements ytterbium and thulium and the group 3 element yttrium, respectively. The molecular structures of monomeric 1-3 exhibit distorted trigonal-bipyramidal coordination environments at the metal center, with the two oxygen atoms of the tetrahydrofuran ligands occupying the axial positions of a trigonal-bipyramidal coordination polyeder. The molecular structure of the scandium compound 4 shows a complex polynuclear heterobimetallic arrangement.     

Solid-state and solution structure of lanthanide complexes of a new nonadentate tripodal ligand containing phenanthroline binding units

The new nonadentate tripodal ligand trenphen (tris[(1,10-phenanthroline-2-carboxamido)-ethyl]amine) has been synthesized by condensation of tren [tris(2-aminoethyl)amine] with an excess of 1,10-phenanthroline-2-carboxylic acyl chloride. The ligand trenphen and its lanthanide complexes (Sm, Nd, Eu, Tb, and Lu) have been structurally characterized by single-crystal X-ray diffractometry. Crystals of trenphen.H2O.CH3CN, 1, are monoclinic, space group P2(1)/n, a = 14.9923(8) A, b = 17.4451(10) A, c = 17.1880(10) A, beta = 114.8290(10) degrees, V = 4079.9(4) A3, Z = 4. The solid-state crystal structures of the isostructural [Ln(trenphen)](OTf)3.yH2O.xEt2O.zCH3CN (OTf = CF3SO3) (Ln = Nd, y = 0.5, x = 1, z = 3 (2); Ln = Sm, y = 0.5, x = 1, z = 3 (3); Ln = Eu, y = 0.5, z = 3 (4); Ln = Tb, y = 0.5, x = 1, z = 1.5 (5); Ln = Lu, y = 0.5, x = 1, z = 1.5 (6)) (trigonal, P-3, Z = 2) show that the covalent tripod trenphen undergoes a rearrangement in the presence of lanthanide ions yielding three tridentate binding units which encapsulate the nine-coordinated lanthanide ion with a slightly distorted, tricapped, trigonal prismatic coordination geometry. The correlation observed between the decrease of Ln-N distances and the metal ionic radius indicates that trenphen, although containing rigid bidentate phenanthroline units, is sufficiently flexible to self-organize without steric constraints around lanthanide ions of different size. Solution-state NMR studies show that complexes 2-6 exist in acetonitrile solution as discrete rigid C3-symmetric species retaining the triple-helical structure observed in the solid state. NMR and ES-MS titration show the formation of bimetallic and trimetallic species in the presence of an excess of metal, whereas mononuclear bistrenphen complexes are obtained in the presence of an excess of ligand.     

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics‐based force fields, although they cannot fully describe protein–ligand interactions. A noteworthy computational method in development involves large‐scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large‐scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange‐correlation functionals, and solvation effects) on the binding energies of the FK506‐binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2‐MP2/6‐31G(d), is suitable for evaluating the protein–ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure–activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein–ligand interaction distance. Our acceleration scheme, which uses FMO2‐HF/STO‐3G:MP2/6‐31G(d) at R_int = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy. © 2015 Wiley Periodicals, Inc.     

Three novel lanthanide complexes with imidazole-4,5-dicarboxylate ligand: Hydrothermal syntheses, structural characterization, and properties

Three novel lanthanide complexes, namely, [Ce(Himdc)(H₂imdc)(H₂O)₃]·H₂O (1), {[Dy(Himdc)(Ox)_0.5(H₂O)₂]·H₂O}_n (2), and {[Nd(Himdc)(Ox)_0.5(H₂O)₂]·H₂O}_n (3) (H₃imdc = imidazole-4,5-dicarboxylic acid, Ox = oxalate), have been successfully prepared by the assembly of lanthanide ions and H₃imdc ligand under different synthetic conditions. All of the complexes have been characterized by means of elemental analysis, IR, TG analysis, luminescence spectroscopy as well as single-crystal X-ray diffraction analysis. The 3D supramolecular structure of 1 is constructed from 1D zig-zag chains through the hydrogen bonding interactions. Complex 2 possesses the chair-shaped secondary building units (SBUs) with Dy₆(Himdc)₄(Ox)₂ and meso-helical chains (P + M), resulting in a novel 2D structure based on the linkages of oxalate ligand. Complex 3 also presents 2D layer structure with uninodal 6-connected net topology, but crystallizes in the different space group and owns higher coordination number of the central metal atom than complex 2. The luminescence property of 2 is investigated in the solid state at room temperature.     

Synthesis,structures and mass spectrometry of lanthanide nitrate complexes with tricyclohexylphosphine oxide

The complexes Ln(NO₃)₃(OPCy₃)₃(EtOH)_x (Cy = cyclohexyl, C₆H₁₁x = 0 for Ln = Eu, Er, x = 0.5 for Ln = La, Nd and x = 1 for Ln = Tm, Yb) have been prepared by reaction of lanthanide nitrates with Cy₃PO in ethanol. The single crystal X-ray structures for Ln = La, Nd, Eu, Er, Tm and Yb are reported. The structures for Ln = La–Eu have two molecules in the unit cell in which the nitrates are all bound as bidentate ligands. The unit cell for Ln = Er contains two distinct molecules; one with three bidentate nitrates and one with two bidentate and one monodentate nitrate. The Tm and Yb complexes have one molecule in the unit cell with two bidentate and one monodentate nitrate ligands. The monodentate nitrates are hydrogen bonded to ethanol in the Tm and Yb structures but not in the Er complex. The infrared spectra of the three classes of complex do not readily permit identification of the monodentate nitrate groups. Electrospray mass spectrometry indicates that redistribution/ionisation reactions occur in solution. Ions formed by solvolysis reactions are attributed to gas phase processes associated with the electrospray technique. Tandem mass spectrometry for the La, Ho and Yb complexes shows that in the gas phase loss of Cy₃PO is the sole fragmentation pathway for all but the Yb complex where the higher energy required for initial fragmentation leads to a more complex fragmentation pattern.     

Structure, resolution and chiroptical analysis of stable lanthanide complexes of a pyridylphenylphosphinate triazacyclononane ligand

Lanthanide complexes of a pyridylphenylphosphinate ligand based on triazacyclononane form an isostructural series. The C(3)-symmetric Δ and Λ complexes of Eu and Tb are strongly emissive and can be resolved by chiral HPLC; the absolute configuration of each complex has been assigned using CD and CPL measurements.     

Ruthenium and chromium complexes bearing pH-indicators as the η6-arene ligand: Synthesis,characterization, and protonation behavior

A series of ruthenium and chromium complexes bearing pH indicators as the η⁶-arene ligand, (η⁶-X)(ML_n)_y [X = methyl yellow, crystal violet lactone, phenolphthalein; ML_n = RuCp¹⁺, RuCl₂(L), Cr(CO)₃; y = 1, 2] is prepared and characterized by spectroscopic and crystallographic methods. Of the plural arene rings in the indicators, a specific arene ring can be successfully coordinated to the metal center in a selective manner under appropriate conditions (i.e. use of the precursors of different oxidation states and reaction with the non-protonated and protonated pH indicator). The obtained indicator complexes show halochromic behavior depending on pH as observed for the parent molecules but the transition pH ranges are shifted to the more acidic side because of the attachment of the electron-withdrawing metal fragments, which decrease the basicity of the attached pH indicators.     

Structural and mechanical properties of alkali hydrides investigated by the first-principles calculations and principal component analysis

The structural and mechanical properties of alkali hydrides (LiH, NaH, KH, RbH, and CsH) were investigated via first-principles calculations which cover the optimized structural parameters. The density functional theory in combination with the generalized gradient approximation (GGA) were used in this study. From the present study, one could note that alkali hydrides are brittle materials and mechanically stable. It was found that stiffness and shear resistance are greater in LiH than in other hydrides. It is more brittle in nature, and comparatively harder than the other materials under study; it also presents a high degree of anisotropy. The results were then investigated and analyzed with principal component analysis (PCA), which is one of the most common techniques in multivariate analysis, was used to explore the correlations among material properties of alkali hydrides and to study their trends. The alkali hydrides obtained by the first-principles calculations were also compared with the alkaline-earth metal hydrides (BeH₂, MgH₂, CaH₂, SrH₂, and BaH₂) and discussed in this work.     

Thermodynamics, structure and properties of polynuclear lanthanide complexes with a tripodal ligand: insight into their self-assembly

Self-assembly processes between a tripodal ligand and Ln(III) cations have been investigated by means of supramolecular analytical methods. At an equimolar ratio of components, tetranuclear tetrahedral complexes are readily formed in acetonitrile. The structural analysis of the crystallographic data shows a helical wrapping of binding strands around metallic cations. The properties of this series of highly charged 3D compounds were examined by using NMR spectroscopy and optical methods in solution and in the solid state. In the presence of excess metal, a new trinuclear complex was identified. The X-ray crystal structure elucidated the coordination of metallic cations with two ligands of different conformations. By varying the metal/ligand ratio, a global speciation of this supramolecular system has been evidenced with different spectroscopic methods. In addition, these rather complicated equilibria were successfully characterised with the thermodynamic stability constants. A rational analysis of the self-assembly processes was attempted by using the thermodynamic free energy model and the impact of the ligand structure on the effective concentration is discussed.