Molecular mechanical calculations of the molecular structure of eight-coordinate europium complexes

Molecular mechanics methods were applied to the determination of the structure of eight-coordinate europium complexes: tris(acetylacetonato)Eu(III) trihydrate, tris(acetylacetonato) (1,10-phenanthroline)Eu(III), and tetrakis(benzoylacetonato)Eu(III). Optimization of MM2 force-field parameters and improvement of the calculation method were carried out using models of the complexes based on X-ray structural investigations. Steric ligandligand interactions in the first coordination sphere were treated as dominant for the lanthanide complexes. The major contributions to the energy are those of nonbonded 1,3-interactions between the atoms directly bound to the europium atom. The results of the calculations agree well with the crystal structures of the mentioned complexes.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1555–1559, September, 1993.     

Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics

A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie-Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d-shell. The quantum mechanical EHCF part is limited to the metal ion d-shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration.     

A molecular packing analysis of some ferrous porphyrin complexes

An analysis has been made of the applicability of various sets of nonbonded interaction potential parameters which do not consider hydrogen atoms explicitly, to represent molecular packing interactions in crystals of ferrous porphyrin complexes, which are models for deoxyhemoglobin. Ordered regions of the structures are well described, but disordered solvent or ligands cause difficulty.     

A thiazole-containing tripodal ligand: synthesis, characterization, and interactions with metal ions and matrix metalloproteinases

A new tripodal ligand, tris[2-(((2-thiazolyl)methylidene)amino)ethyl]amine (Tatren), has been synthesized and characterized by NMR, IR, and UV-visible absorbance spectroscopy and elemental analysis. Tatren forms stable complexes with transition metal ions (Zn(2+), 1; Mn(2+), 2; Co(2+), 3) and the alkaline earth metal ions (Ca(2+), 4; Mg(2+), 5). Single-crystal X-ray structures of 1, 2, and 5 revealed six-coordinate chelate complexes with formula [M(Tatren)](ClO(4))(2) in which the metal centers are coordinated by three thiazolyl N atoms and three acyclic imine N atoms. Crystals of 1, 2, and 5 are monoclinic, P2(1)/c space group. Crystals of 4 are triclinic, P space group. The Ca(2+) complex is eight-coordinate with all N atoms of Tatren and one water molecule coordinated to the metal ion. Spectrophotometric titrations show that formation constants for the chelates of metal ions are >1 in methanol. Free Tatren inhibits the catalytic domain of matrix metalloproteinase-13 (MMP-13, collagenase-3) with K(i) = 3.5 +/- 0.6 microM. Molecular mechanics-based docking calculations suggest that one leg of Tatren coordinates to the catalytic Zn(2+) in MMPs-2, -9, and -13 with significant hydrogen bonding to backbone amide groups. High-level DFT calculations suggest that, in the absence of nonbonded interactions between Tatren and the enzyme, the most stable first coordination sphere of the catalytic Zn(2+) is achieved with three imidazolyl groups from His residues and two imine N atoms from one leg of Tatren. While complexes (1-3) do not inhibit MMP-13 to a significant extent, 4 does (K(i) = 30 +/- 10 microM). Hence, this study shows that tripodal chelating ligands of this class and their Ca(2+) complexes have potential as active-site inhibitors for MMPs.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

Syntheses and crystal structures of rubidium and cesium 3,5-dinitropyrid-2-onate, 3,5-dinitropyrid-4-onate and 3,5-dinitro-4-pyridone-N-hydroxylate

Six complexes, rubidium and cesium 3,5-dinitropyrid-2-onate (2DNPO), 3,5-dinitropyrid-4-onate (4NDPO), 3,5-dinitropyrid-4-one-N-hydroxylate (4DNPNO), were synthesized and characterized by elemental analysis, FT-IR, TG-DTG and X-ray single-crystal diffraction analysis. All the complexes crystallized from water and one of them was a hydrate. Rubidium 3,5-dinitropyrid-4-one-N-hydroxylate was crystallized with the 1?:?2 stoichiometry as Rb[H(4DNPNO)₂] upon absorption of carbon dioxide. The structural determinations showed that the coordination sphere around a metal centre is made up of oxygen atoms and nitrogen atoms, except for the 4DNPNO complexes, where the coordination sphere accommodates exclusively oxygen atoms. The coordination numbers of the metal centers vary from 8, 10, 11 to 12, while the ligands, each employing its pyridone tautomer, link with metal cations. Bridging oxygen atoms play an important role in construction of two- and/or three-dimensional networks of these complexes. Hydrogen bonding contributes to the connectivity within a given sheet in Rb[H(4DNPNO)₂]; aromatic π–π stacking interactions exist only in Cs(4DNPNO). The interactions between metal atoms and ligands are generally very weak. The organization of all layer structures appears to be governed mainly by steric effects and electrostatic forces with very little directional influence of the cations. The thermogravimetric analyses of these complexes showed the following consecutive processes: loss of NO₂ groups, collapse of the pyridyl ring backbones and finally inorganic residue formation. These complexes could be used as probes in template effects of heavy alkali-metal cations in the organization of biorelevant ligands and as environment-friendly energetic catalysts in solid propellants.     

Blue dimetallic complexes of two heavy metal ions Cd(II) and Hg(II) with an extended nitrogen donor ligand. Preparation, spectral characterization, and crystallographic studies

In methanol, the metal salts CdCl2.H2O and HgCl2 react instantaneously with the deprotonated ligand, L-, producing molecular dimetallic ink-blue complexes of general formula M2Cl2L2, M=Cd(II), (1) and Hg(II), (2) (HL=2-[2-(pyridylamino)phenylazo]pyridine). Crystal structures of these two complexes are reported. The coordination sphere around each Cd(II) ion in 1 is a distorted square pyramidal. The metal ion (Cd1) sits above the basal plane of three nitrogen atoms, N(1), N(3), and N(4). The second cadmium ion (Cd2) in this compound lies below the plane of three nitrogen atoms, N(6), N(8), and N(9). The apical positions are occupied by two Cl atoms. Secondary intramolecular interactions between the metal ions and the anionic secondary amine nitrogen atoms (N(4) and N(9)) are noted. The geometry of each Hg(II) ion in the mercury complex, Hg2Cl2L2.0.5H2O, is also distorted square based pyramid with the metal ions lying out of planes of the three nitrogen atoms of the chelating ligands. Secondary Hg(1)...N(1A) (deprotonated amine) interactions are noted. The separation between the two Hg(II) ions in this complex is within the sum of their van der Waals radii. Solution properties of these blue complexes are reported. The origin of the intense blue color in these complexes is the intraligand transitions that occur near 615 nm. 1H NMR of Hg2Cl2L2.0.5H2O indicates that it undergoes exchange in solution with the coordinated ligands.     

Structures of lanthanide shift reagent complexes by molecular mechanics computations

Molecular mechanics calculations have been applied to the structure determination of 7-coordinate lanthanide complexes. To circumvent problems in defining oxygen—lanthanide—oxygen bond angles, the energy of angle deformations at the metal center are not evaluated explicitly. Instead the standard approach to molecular mechanics calculations is modified by including 1,3-nonbonded interactions between atoms that are both bonded to the metal center. Geometry optimization for two known lanthanide complexes afforded structures that are in reasonable agreement with X-ray crystal structures, and small discrepancies are attributed to cyrstal packing forces.     

Systematic structural coordination chemistry of p-tert-butyltetrathiacalix[4]arene: 1. Group 1 elements and congeners

Determinations of the crystal structures of complexes of the alkali metal ions with, in the case of Li, the dianion and, in the cases Na-Cs, the monoanion of p-tert-butyltetrathiacalix[4]arene have shown that both the sulfur atoms which form part of the macrocyclic ring, as well as the pendent phenolic/phenoxide oxygen donor atoms, are involved in coordination to these metals. Although the Li and Na complex structures are similar to those of the corresponding complexes of p-tert-butylcalix[4]arene, there is no similarity in the structures of the Cs complexes, with the present structure showing no evidence of polyhapto Cs(+)-pi interactions. Instead, the complex crystallizes as a ligand-bridged (S-, O-donor) aggregate of three Cs ions, solvent molecules, and four calixarenes, somewhat like the Rb complex, though here four Rb ions are present, and higher in aggregation than the K+ complex, where two K+ ions are sandwiched between two calixarene moieties. The triethylammonium complex of the thiacalixarene monoanion, though formally analogous in that it involves a monocation, has a simpler structure than any of the alkali metal derivatives, based formally on proton coordination (H-bonding). However, interestingly, it can be isolated in both solvated (dmf, dmso) and unsolvated forms, as indeed can the "free", p-tert-butyltetrathiacalix[4]arene ligand itself.     

Crystal structures of rubidium and cesium anthranilates and salicylates

In an attempt to probe a potential template role of the large alkali-metal cations rubidium and cesium in the organization of biorelevant ligands, salicylate and anthranilate complexes of the two elements were prepared and structurally investigated. The studies were also expected to show the marked structural differences compared to the corresponding thallium(I) compounds. Rubidium anthranilate and cesium salicylate could be crystallized as the monohydrates Rb(Anth)(H(2)O) and Cs(Sal)(H(2)O). Both have layer structures containing the cations and the polar groups of the ligands in core domains sandwiched by the aromatic rings above and below. The metal atoms have coordination numbers 7 and 8, respectively, with an irregular coordination sphere made up exclusively of oxygen atoms. Crystalline material with a 1:2 stoichiometry, Cs[H(Anth)(2)], is obtained from aqueous solutions of Cs(Anth) upon absorption of carbon dioxide with concomitant formation of cesium bicarbonate, Cs(HCO(3)). The crystal structure of Cs(HCO(3)) was redetermined to obtain precise benchmark data for cesium carbonates and carboxylates. The cesium hydrogen bisanthranilate also has a layer structure with eight-coordinate cesium atoms. The coordination sphere includes one nitrogen donor atom. The organization of all layer structures appears to be governed mainly by steric effects and electrostatic forces with very little directional influence of the cations. This result suggests that the large alkali metals have no efficient template effect for the organization of biological substrates and can explain the low toxicity of rubidium and cesium salts.     

Energetics of the first and second coordination spheres of transition metal ions

For complexes of transition metals (manganese, iron, cobalt, nickel) with monodentate ligands, equilibrium metal-ligand distances and ligand bond energies in the first and second coordination spheres have been calculated by the CNDO method. Some effects of ligand bond energies in different coordination spheres are analyzed. These effects significantly differ between the first and second coordination spheres. In the first sphere, the ligand bond energy is mainly determined by the nature of the central ion and the type of donor atom of the ligand, but weakly depends on the structure of the ligand. Conversely, in the second coordination sphere, the ligand bond energy weakly depends on the nature of the central ion and the type of donor atom, but considerably depends on the structure of the ligands in the first coordination sphere. In the second coordination sphere, ligand binding is determined by ligand interactions with both the central ion and the ligands of the first sphere. In the general case, when strong specific interactions between ligands are absent, the energetics of the second sphere is determined by the size of the inner-spheric ligands, which may be considered to be a specific steric effect. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 370–374, March–April, 1995. Translated from L. Smolina     

Conformational/configurational analysis of all the binding geometries of cobalt(III) bleomycin

No crystal structure of metallobleomycin (BLM) exists, and the exact coordination mode of the ligand is unknown. To date, spectroscopic investigations of BLM complexes and crystal structures of BLM models have been used to propose its metal coordination sites. This has led to contradictory interpretations of the metal coordination sphere in BLM. Inorganic molecular mechanics and configurational/conformational searches were used to analyze HOO-CoBLM A2, H2O-CoBLM A2, and HOO-CoPEP with commonly proposed binding geometries. The lowest energy binding geometry found was one with the mannose carbamoyl bound to the cobalt ion. The Monte Carlo dihedral and translational variational searches were able to find most of the configurations available to cobalt(III) bleomycin in the three binding geometries examined.     

Noncovalent Interactions at Lanthanide Complexes

Lanthanide complexes have attracted a widespread attention due to their structural diversity, as well as multifunctional and tunable properties. The development of lanthanide based functional materials has often relied on the design of the secondary coordination sphere of the corresponding lanthanide complexes. For instance, usually simple lanthanide salts (solvento complexes) do not catalyze effectively organic reactions or provide low yield of the expected product, whereas the presence of a suitable organic ligand with a noncovalent bond donor or acceptor centre (secondary coordination sphere) modifies the symmetry around the metal centre in lanthanide complexes which then successfully can act as catalysts in both homogenous and heterogenous catalysis. In this minireview, we discuss several relevant examples, based on X-ray crystal structure analyses, in which the hydrogen, halogen, chalcogen, pnictogen, tetrel and rare-earth bonds, as well as cation-π, anion-π, lone pair-π, π–π and pancake interactions, are used as a synthon in the decoration of the secondary coordination sphere of lanthanide complexes.     

Relating structural and thermodynamic effects of the Pb(II) lone pair: a new picolinate ligand designed to accommodate the Pb(II) lone pair leads to high stability and selectivity

The crystal and molecular structure and the stability of lead and calcium complexes of two chelates containing picolinate chelating groups in different geometries have been investigated in order to relate the ligand affinity and selectivity for lead over calcium with the ability of the ligand to accommodate a stereochemically active lone pair. The crystal structures of the lead complexes of the diprotonated and monoprotonated tripodal ligand tpaa2- show that the three picolinate arms of the tripodal ligand coordinate the lead in an asymmetric way leaving a gap in the coordination sphere to accommodate the lead lone pair. As a consequence of this binding mode, one picolinate arm is very weakly bound and therefore can be expected to contribute very little to the complex stability. Conversely, the geometry of the dipodal ligand H2dpaea is designed to accommodate the lead lone pair; in the structure of the [Pb(dpaea)] complex the donor atoms of the ligand occupy only a quarter of the coordination sphere, reducing the sterical interaction between the lead lone pair with respect to the H3tpaa complexes. As a result, in the lead structures of H2dpaea all the ligand donor atoms are strongly bound to the metal ion leading to increased stability. The high value of the formation constant measured for the lead complex of the dipodal dpaea2- (log beta11(Pb)=12.1(3)) compared to the lower value found for the one of the tripodal tpaa3- (log beta11(Pb)=10.0(1)) provides direct evidence of the influence of the stereochemically active lead lone pair on complex stability. As a result, since the ligand geometry has little effect on the stability of the calcium complex, a remarkable increase in the Pb/Ca selectivity is observed for dpaea-(10(6.6)) compared to tpaa3- (10(1.5)), making the dipodal ligand a good candidate for application as extracting agent for the lead removal from contaminated water.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.     

1,10-Phenanthroline: A versatile building block for the construction of ligands for various purposes

This review will cover the developments in the chemistry of phenanthroline-based ligands in the last 10–15 years. 1,10-Phenanthroline (phen) is a classic ligand in coordination chemistry, which couples versatility in metal ion binding with peculiar properties of its complexes. For instance, metal complexes with phenanthroline can be featured by an intense luminescence or can interact with DNA in an intercalative fashion inducing, in some cases, DNA cleavage. For this reason a number of phenanthroline-containing ligands has been recently synthesized by inserting phenanthroline within open-chain or macrocyclic backbone, in order to develop new molecular chemosensors for metal cations and anions, ionophores as well as new intercalating agents for polynucleotides. Furthermore, phenanthroline is rigid and its insertion within cyclic or acyclic structures can impart to the resulting ligand a high degree of pre-organization, affording selective complexing agents. This review will discuss on the coordination, luminescence and intercalating and/or DNA cleaving properties as well as on analytical applications of metal complexes with phenanthroline-based ligands. Particular attention will be devoted to macrocyclic receptors or open-chain ligands that, beside the phenanthroline nitrogen atoms, contain other donor atoms able to interact with the metal cations or anions.     

Molecular mechanics studies of the conformations of metal complexes of 1,4,7,10,13,16-hexaazacyclooctadecane: Calculations of macrocyclic cavity size

Molecular mechanics calculations are reported on metal complexes of 18-azacrown-6. Four possible conformations are considered which encapsulate the metal in different geometric environments, namely, chiral octahedral, meso octahedral, trigonal prismatic, and hexagonal bipyramidal. Crystal structures are available for all but the last geometry, and molecular mechanics calculations show an excellent fit to the experimental data. The strain energy of the macrocycle has been calculated for a range of M-N distances, and thus the hole size of the macrocycle has been obtained for various conformations. Two different methods were used to calculate the strain energy of the metal environment. We either used the conventional molecular mechanics term for angle bending,k _b — ₀)², and chose the ideal angles to fit the particular metal geometry, or we set the angle force constants to zero and introduced 1,3 van der Waals interactions between the ligand donor nitrogen atoms. Results from the two methods are compared.     

A novel decomposition of torsional potentials into pairwise interactions: A study of energy second derivatives

A general method of analyzing intramolecular torsional potentials in terms of energy second derivatives that couple the rotating atoms is presented. The method offers a rigorous decomposition of the total torsional potential into pairwise (dihedral) interactions and enables one to derive nonbonded torsional interactions between 1–4 atoms as well as between more distant atoms and sites. The method is demonstrated on ethane, propane and acetaldehyde. It is shown that the 1–4 H…H dihedral potentials in ethane and propane are very similar, thereby supporting the notion of transferable force field potential functions. However, the dihedral potentials that are obtained differ from 1–4 potentials that are used in current force fields. Intramolecular three body effects are clearly seen in this method and are found to be relatively large for the dihedral interactions, although in the one case studied (propane) the overall effect on the methyl-methyl interaction is negligible due to cancellation of terms. The analysis explicitly shows that the barrier in acetaldehyde is due mainly to the dihedral H…H interaction.