First linear alignment of five C-Se...O...Se-C atoms in anthraquinone and 9-(methoxy)anthracene bearing phenylselanyl groups at 1,8-positions

Five Ci-Se...O...Se-Ci atoms in anthraquinone and 9-(methoxy)anthracene bearing phenylselanyl groups at 1,8-positions align linearly, the origin of which is shown to be a nonbonded 5c-6e interaction of the five atoms.     

Nonbonded P···P and P···Se Interactions in Naphthalene 1,8-Positions: Role of Lone-Pair Orbitals

The lone pair-lone pair repulsion plays an important role in the nonbonded P;;;P interaction in naphthalene 1,8-positions. The conformations around P and Se in 8-(PhSe)-1-(Ph 2 P=O)C 10 H 6 are determined by the attractive O;;;Se--C 3c-4e type interaction. The P;;;Se interaction in the 1,8-positions is also discussed.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH₂r united atoms of the cyclohexane ring, and one representing three FG CH₂r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.     

Extended hypervalent 5c-6e interactions: linear alignment of five C-Se---O---Se-C atoms in anthraquinone and 9-methoxyanthracene bearing arylselanyl groups at the 1,8-positions

The structures of 1,8-bis(phenylselanyl)anthraquinone (1a), 1,8-bis(phenylselanyl)-9-methoxyanthracene (2a), and 1,8-bis(phenylselanyl)anthracene (3a) are determined by X-ray crystallographic analysis, together with the derivatives. The Se-C(i) (Ph) bonds in 1a are placed on the anthraquinone plane (both type B) and the phenyl planes are perpendicular to the anthraquinone plane. The structure around the Se atoms in 2a is very close to that of 1a: the conformations of the PhSe groups are both type B. Consequently, the five C(i)-Se- - -O- - -Se-C(i) atoms in 1a and 2a align linearly. The nonbonded Se- - -O distances in 1a and 2a are 2.673-2.688 and 2.731-2.744 A, respectively, which are about 0.7 A shorter than the sum of van der Waals radii of the atoms. The extended hypervalent sigma*(C(i)-Se)- - -n(p)(O)- - -sigma*(Se-C(i)) 5c-6e interactions are strongly suggested for the origin of the linear alignment of the five atoms in 1a and 2a. The 5c-6e must be constructed by the connection of the two hypervalent n(p)(O)- - -sigma*(Se-C(i)) 3c-4e interactions through the central n(p)(O). The five C(i)-Se- - -H- - -Se-C(i) atoms never align linearly in 3a. To reveal the nature of 5c-6e in 1a and 2a, QC calculations are performed on H(a)H(b)(A)Se- - -O([double bond]CH(2))- - -(B)SeH(a')H(b') (model a) and H(a)H(b)(A)Se- - -OH(2)- - -(B)SeH(a')H(b') (model b) with the B3LYP/6-311++G(3df,2pd) method, where the nonbonded Se- - -O distances are fixed at 2.658 A. Four conformers, a (AA-cis), a (AA-trans), a (AB), and a (BB), are optimized to be stable for model a, where a (AA) shows both type A for the (A)Se-H(b) and (B)Se-H(b') bonds in model a. Three conformers, b (AA-cis), b (AB), and b (BB), are stable for model b. The bonding models in AA, AB, and BB correspond to 3c-6e, 4c-6e, and 5c-6e, respectively. The models become more stable by 42 +/- 5 kJ mol(-1), if the type A conformation of each Se-H bond changes to type B. No noticeable saturation is observed in the stabilization for each change. QC calculations are also performed on 1a-3a at the B3LYP level. Three conformers are evaluated to be stable for 1a and 2a. The relative energies of 1a (AA-trans), 1a (AB), and 1a (BB) are 0.0, -31.5, and -60.6 kJ mol(-1), respectively, and those of 2a (AA-cis), 2a (AB), and 2a (BB) are 0.0, -24.4, and -36.5 kJ mol(-1), respectively. These results demonstrate that the origin of the linear alignment of the five C-Se- - -O- - -Se-C atoms in 1a and 2a is the energy lowering effect by the extended hypervalent 5c-6e interactions of the sigma*(C-Se)<--n(p)(O)-->sigma*(Se-C) type. The pi-conjugation between pi(C[double bond]O) and n(pz)(Se) through the pi-framework of anthraquinone must also contribute to stabilize the BB structure of 1a, where z is the direction perpendicular to the anthraquinone plane.     

Conformational study of Co(II), Ni(II), and Cr(III) complexes of the edta-type: Crystal structure of 1D polymeric trans(O)-Ba[Co(1,3-pddadp)] · 8H2O complex stabilized by infinite water tapes

The trans(O⁶) isomer of the Ba[Co(1,3-pddadp)] · 8H₂O complex (where 1,3-pddadp represents hexadentate 1,3-propanediamine-N,N′-diacetate-N,N′-di-3-propionate ion) has been prepared and characterized by X-ray crystallography. In the crystal structure the complex cations and anions are bridged by carboxylate oxygen atoms from the in-plane coordinated glycinate rings (G-rings) of [Co(1,3-pddadp)]²⁻ and by the barium-coordinated water molecules, thus forming 1D polymeric chains, separated by infinite water tapes hydrogen bonded to the [Co(1,3-pddadp)]²⁻ carboxylate oxygens from the out-of-plane β-alaninate rings (R-rings). Conformational analysis of the three possible geometrical isomers: trans(O⁵), trans(O⁵O⁶), and trans(O⁶) of the [Co(1,3-pddadp)]²⁻ complex, with ligand acting as hexadentate, as well as of the corresponding complexes of Ni(II) and Cr(III) has been performed using the consistent force field (CFF) method, with the parameters developed previously for edta-type complexes of chromium(III) and supplemented with new parameters for cobalt(II) and nickel(II). The energy-minimized structure of the trans(O⁵O⁶) isomer represents the global minimum for the [M(1,3-pddadp)]ⁿ⁻ (M = Co(II), Ni(II), and Cr(III)) species. The occurrence of the least energetically favored trans(O⁶) isomer in a crystal and the exceptional conformation of the axially oriented β-alaninate rings can be accounted for by the stabilizing role of the infinite tapes of planar cyclic water pentamers and hexamers which act as a “glue” to reinforce the coordination polymeric chains.     

Products of the reactions of sparteine-2-thione with CuBr2 in protic and aprotic solvents

Reactions of copper(II) bromide with racemic sparteine-2-thione (SSp) in a 1:1 M ratio yielded two new complexes, whose structures depend on the solvent used. In acetonitrile, the reaction product is a sulfur-bridged dinuclear [CuBr₂(μ-SSp)]₂ complex (1) in which sparteine-2-thione acts as a bridging S-ligand, while in methanol it is a CuBr₂ complex (2) with sparteine deprived of the A-ring. Compound 1 crystallizes as an acetonitrile solvate in a 1:2 ratio and constitutes one of a few Cu(II) doubly bridged heterocyclic thionato complexes. The disorder of the C/D bisquinolizidine fragment in the crystal of 1 reflects the ease of the conversion from the common trans boat-chair to the unprecedented cis chair-boat stereoisomer. Obtained in methanol, the sparteine surrogate (Sp(surr)), is equally effective as a chelating ligand as sparteine and its isomers, and thus can be used as an alternative diamine ligand in metal complexation. Metal coordination with Sp(surr) brings the diamine nitrogens much closer together than in any other sparteine metal complexes.     

A study of the reactions of methionine- and histidine-containing peptides with palladium(II) complexes: The key role of steric crowding on palladium(II) in the selective cleavage of the peptide bond

¹H NMR spectroscopy was applied to study the reactions of palladium(II) complexes, cis-[Pd(dpa)Cl₂] and cis-[Pd(dpa)(H₂O)₂]²⁺ (dpa is 2,2′-dipyridylamine acting as a bidentate ligand) with the dipeptides methionylglycine (Met-Gly) and histidylglycine (His-Gly), and the N-acetylated derivatives of these dipeptides, MeCOMet-Gly and MeCOHis-Gly. All reactions were carried out in the pH range 2.0–2.5 with equimolar amounts of the palladium(II) complex and the peptide at two different temperatures, 25 and 60 °C. In the reactions of cis-[Pd(dpa)Cl₂] and cis-[Pd(dpa)(H₂O)₂]²⁺ with Met-Gly and His-Gly, no hydrolysis of the peptide bond was observed. The final product in these reactions was the [Pd(dpa)₂]²⁺ complex. The square-planar structure of this complex was confirmed by X-ray analysis. The reaction of the cis-[Pd(dpa)(H₂O)₂]²⁺ complex with the MeCOHis-Gly and MeCOMet-Gly peptides under the previously mentioned experimental conditions was remarkably selective in the cleavage of the amide bond involving the carboxylic group of methionine in the side chain. The modes of coordination of cis-[Pd(dpa)Cl₂] and cis-[Pd(dpa)(H₂O)₂]²⁺ in the reactions with the non-acetylated peptides and the total steric inhibition of the hydrolytic reaction between cis-[Pd(dpa)(H₂O)₂]²⁺ and MeCOHis-Gly can be attributed to the steric bulk of the palladium(II) complex. This finding should be taken into consideration in designing new palladium(II) complexes for the regioselective cleavage of peptides and proteins.     

Extended Hypervalent 5c–6e Interactions: Linear Alignment of Five C─Z- - -O- - -Z─C (Z = S,Se) Atoms in Anthraquinone and Anthracene Systems

Abstract

Structures of 1,8-(ArZ)₂C₁₄H₆O₂ and 9-(MeO)-1,8-(ArZ)₂C₁₄H₇ (Z = S, Se) are determined by X-ray crystallographic analysis. Five C─Z- - -O- - -Z─C atoms of the compounds align linearly, which are analyzed by the extended hypervalent 5c–6e model, based on QC calculations. CT of the 5c–6e occurs as the σ^*(C─Z) ← n _p (O)→ σ*(Z─C) direction.     

Synthesis,characterization and antimicrobial activity of Ni(II) and Zn(II) complexes with N′,N′-bis[(1E)-1-(2-pyridyl)ethylidene]propanedihydrazide. Crystal structures of two highly solvated bimetallic complexes of Ni(II)

The bimetallic [Ni₂(H₂L2)₂](ClO₄)₄ (1), [Ni₂(HL2)(H₂L2)](ClO₄)₃ (2) and [Zn₂(H₂L2)₂](BF₄)₄ (3) complexes (H₂L2 = N′,N′²-bis[(1E)-1-(2-pyridyl)ethylidene]propanedihydrazide) were synthesized and characterized. The structure of complexes (1) and (2) was established by X-ray analysis. NMR spectroscopy was used for the characterization of complex (3). The complexes (1) and (2) were obtained from the same synthetic reaction and two crystal types of these complexes have been isolated during the fractional crystallization process.