Dependence of the optical absorption and Na+ binding energies of coumarin-crown ethers on the size and attachment position of ether ring: density functional investigation

The crowned coumarin complexes are well known compounds for their ion recognition abilities. They undergo photophysical changes upon cation binding. On the basis of density functional theory calculations, we examined the sodium cation (Na⁺) binding energies of coumarin-crown ethers based on 15-Crown-5 (15 C5) and 18-Crown-6 (18 C6) as well as the optical absorptions of coumarin-crown ethers based on 12-Crown-4 (12 C4), 15 C5 and 18 C6. We explored why the attachment of crown ether ring to coumarin affects the Na⁺ binding energies of coumarin-crown ethers and also why the optical absorption of coumarin is modified by the crown ethers. Our study reveals that the Na⁺ ion binding energies of coumarin-crown ethers depend strongly on the size of the crown ether ring and also on the attachment position of the ether ring on coumarin. These factors affect the intramolecular charge transfer and overall stability of the complexes. The absorptions of the coumarin and ether ring parts of coumarin-crown ether are red shifted from those of isolated coumarin and crown ether, respectively. The red-shift of the coumarin ester group absorption is much stronger depending on the attachment position of the ether ring to coumarin. The absorption intensity of the coumarin part in coumarin-crown ethers is reduced for the benzene group absorption, but is enhanced for the ester group absorption.

Specificities of cation permeabilities induced by some crown ethers in mitochondria.

A series of macrocyclic crown ethers have been assayed as ionophores using respiring rat liver mitochondria, and the same compounds have been subjected to physicochemical investigation. Association constants and stoichiometries for the complexes with potassium, rubidium, and cesium were measured in methanol. Rates of transport of potassium bromide through aqueous/organic/aqueous systems and the partition coefficient from water into the organic phase were also measured and found to be in the same rank order as the association constants. Effective uptake by the mitochondria was clearly correlated with the complexing by the cation by one or more molecules of ionophore. Thus, for all three cations the most effective compound was the largest, i.e., di-t-butyldibenzo-30-crown-10, capable of wrapping around the cation. Other compounds giving measurable uptake were those which form sandwich complexes, one cation to two crown molecules; those containing five oxygen atoms induced greater uptake of potassium than of the other two alkali metals, while compounds containing six or seven oxygen atoms had greater effects on cesium or rubidium than on potassium. Within a structurally similar series of compounds the rank orders for uptake differed from those for the association constants; in particular, compounds having one benzene ring on an 18-membered crown compound were ineffective on all cations studied; effective compounds contained two benzene rings. In contrast to X-537A and A23187, none of the compounds caused release of magnesium from the mitochondria.     

DFT study of a series of crown-4 ethers and their selectivity trend for alkali metal cations: Li+ and Na+

The molecular and electronic structures for 12- to 16-crown-4 (named 12C4, 13C4, 14C4, 15C4, 16C4, respectively) and 2,3,5,6,8,9-hexahydrobenzo[b][1,4,7,10]tetraoxacyclododecine (B12C4) 3,5,6,7,9,10-hexahydro -2H-benzo[e][1,4,7,10]tetraoxacyclotridecine (B13C4) and their complexes with alkali metal cations Li⁺ and Na⁺ have been explored using the density functional theory (DFT) with B3LYP/ 6–31G* method. The nucleophilicity of crown-4 ethers has been investigated by the Fukui function. Their selectivity trend shows that of all the crown-4 ethers, 14C4 shows the highest cation selectivity for Li⁺ over Na⁺, has been achieved on the basis of thermodynamic analysis. In addition, Li⁺/crown-4 series are more stable than Na⁺/crown-4 series in the gas phase. The calculated results are in good agreement with the experimental observation.     

DFT modeling on the suitable crown ether architecture for complexation with Cs<Superscript>+</Superscript> and Sr<Superscript>2+</Superscript> metal ions

Crown ether architectures were explored for the inclusion of Cs⁺ and Sr²⁺ ions within nano-cavity of macrocyclic crown ethers using density functional theory (DFT) modeling. The modeling was undertaken to gain insight into the mechanism of the complexation of Cs⁺ and Sr²⁺ ion with this ligand experimentally. The selectivity of Cs⁺ and Sr²⁺ ions for a particular size of crown ether has been explained based on the fitting and binding interaction of the guest ions in the narrow cavity of crown ethers. Although, Di-Benzo-18-Crown-6 (DB18C6) and Di-Benzo-21-Crown-7 (DB21C7) provide suitable host architecture for Sr²⁺ and Cs⁺ ions respectively as the ion size match with the cavity of the host, but consideration of binding interaction along with the cavity matching both DB18C6 and DB21C7 prefers Sr²⁺ ion. The calculated values of binding enthalpy of Cs metal ion with the crown ethers were found to be in good agreement with the experimental results. The gas phase binding enthalpy for Sr²⁺ ion with crown ether was higher than Cs metal ion. The ion exchange reaction between Sr and Cs always favors the selection of Sr metal ion both in the gas and in micro-solvated systems. The gas phase selectivity remains unchanged in micro-solvated phase. We have demonstrated the effect of micro-solvation on the binding interaction between the metal ions (Cs⁺ and Sr²⁺) and the macrocyclic crown ethers by considering micro-solvated metal ions up to eight water molecules directly attached to the metal ion and also by considering two water molecules attached to metal-ion-crown ether complexes. A metal ion exchange reaction involving the replacement of strontium ion in metal ion-crown ether complexes with cesium ion contained within a metal ion-water cluster serves as the basis for modeling binding preferences in solution. The calculated O-H stretching frequency of H₂O molecule in micro-solvated metal ion-crown complexes is more red-shifted in comparison to hydrated metal ions. The calculated IR spectra can be compared with an experimental spectrum to determine the presence of micro-solvated metal ion–crown ether complexes in extractant phase.     

Stabilities in nitromethane of alkali metal ion complexes with dibenzo-18-crown-6 and dibenzo-24-crown-8 and their transfer from nitromethane to other polar solvents

Stability constants for the 1:1 complexes of Na⁺, K⁺, Rb⁺, and Cs⁺ with dibenzo-18-crown-6 (DB18C6) and dibenzo-24-crown-8 (DB24C8) have been determined by conductometry at 25 °C in a poorly solvating solvent, nitromethane. For both the crown ethers, the stability constant decreases with increasing metal ion size, Na⁺ > K⁺ > Rb⁺ > Cs⁺, regardless of the size compatibility between the metal ions and the ligand cavities. A comparison of the results with those in several other solvents (S: acetonitrile, propylene carbonate, water, methanol, and N,N-dimethylformamide) leads to the conclusion that the selectivity sequence of these crown ethers in nitromethane agrees with the intrinsic one in the absence of a solvent. Transfer activity coefficients of the crown ethers and their complexes from nitromethane to S have been determined to evaluate the solute-solvent interactions. It is shown that DB24C8 shields the alkali metal ions more effectively from the solvents than DB18C6 because of the larger number of oxygen atoms and the more flexible structure of DB24C8. Regarding the complexation in nitromethane as a reference, the complex stability and selectivity in S are discussed. The selectivities of these crown ethers in water, methanol, and N,N-dimethylformamide, which apparently obey the size-fit concept, are largely due to the solvation of the free alkali metal ions.     

Complexation of alkali metal cations by crown-ether type podands with applications in solvent extraction: insights from quantum chemical calculations

The complexation behavior of nine polyether type podands with a varying number of oxygen donor atoms (4–10) towards the alkali metal cations Li⁺, Na⁺ and K⁺ was studied by quantum chemical methods at the DFT-B3LYP level of theory using the all-electron split-valence 6-311++G(d,p) basis set. The optimized structures of the complexes show a regular increase in the mean cation–oxygen distance with the coordination number. OC–CO dihedral angles of the podand arms were also found to increase with the coordination number and with the size of the cation. Maximum values for the number of strong cation–oxygen interactions (effective coordination numbers) were found for each cation (six for Li⁺, seven for Na⁺ and eight for K⁺). The calculated values for thermodynamic parameters relative to the binding of free and solvated cations to the podands allowed the assessment of binding constants in vacuum, in water and in dichloromethane. The estimated cation extraction constants mimic the experimental extraction trends, but their values are much larger than experimental values. Scale factors were determined to correct the values effectively. For each podand the ratios between the calculated extraction constants of Li⁺ (or Na⁺) and the corresponding ones for K⁺ (seen as extraction selectivities) compare acceptably with the corresponding experimental values.     

Effect of second-sphere coordination 12. Adduct formation behavior of crown ethers with ammine complexes of ruthenium containing a protic ligand of other type than ammine

Adduct formation of pentaammineruthenium complexes involving a different type of protic ligand, such as imidazole, was investigated for a series of crown ethers with different ring size. Changes in redox potential and in absorption spectra of the complex were measured on addition of crown ether to the complex solution. The magnitude of the change in both properties is dependent on the ring size of crown ethers. ¹H-NMR spectra of the complex were measured in the presence of crown ethers in order to elucidate hydrogen bonding sites. The chemical shifts of NH proton of imidazol and ammine protons were measured at various concentrations of crown ethers. Adduct formation was discussed based on the features of dependences of those chemical shifts on crown ether concentration.     

Theoretical study of crown ethers with incorporated azobenzene moiety

A series of crown ethers containing the azobenzene moiety incorporated into crowns of various sizes [Cr(O₆)_, Cr(O₇) and Cr(O₈)] and their corresponding alkali metal cation (Li⁺, Na⁺, K⁺, Rb⁺) complexes have been studied theoretically. The density functional theory (DFT) method was employed to elucidate the stereochemical structural natures and thermodynamic properties of all of the target molecules at the B3LYP/6-31 G(d) and LANL2DZ level for the cation Rb⁺. The fully optimized geometries had real frequencies, thus indicating their minimum-energy status. In addition, the bond lengths between the metal cation and oxygen atoms, atomic torsion angles and thermodynamic energies for complexes were studied. Natural bond orbital (NBO) analysis was used to explore the origin of the internal forces and the intermolecular interactions for the metal complexes. The calculated results show that the most significant interaction is that between the lone pair electrons of electron-donating oxygens in the cis-forms of azobenzene crown ethers (cis-ACEs) and the LP* (1-center valence antibond lone pair) orbitals of the alkali-metal cations (Li⁺, Na⁺, K⁺ and Rb⁺). The electronic spectra for the cis-ACEs [cis-Cr(O₆), cis-Cr(O₇) and cis-Cr(O₈)] are obtained by the time-dependent density functional theory (TDDFT) at the B3LYP/6-31 G(d) level. The spectra of the cis-isomers show broad π → π* (S₀ → S₂) absorption bands at 310–340 nm but weaker n → π* (S₀ → S₁) bands at 480–490 nm. The calculated results are in good agreement with the experimental results.     

A theoretical investigation of the interactions between hydroxyl-functionalized ionic liquid and water/methanol/dimethyl sulfoxide

Density functional calculations have been used to investigate the interactions of 1-(2-hydroxyethyl)-3-methylimidazolium ([C₂OHmim]⁺)-based ionic liquids (hydroxyl ILs) with water (H₂O), methanol (CH₃OH), and dimethyl sulfoxide (DMSO). It was found that the cosolvent molecules interact with the anion and cation of each ionic liquid through different atoms, i.e., H and O atoms, respectively. The interactions between the cosolvent molecules and 1-ethyl-3-methylimizolium ([C₂mim]⁺)-based ionic liquids (nonhydroxyl ILs) were also studied for comparison. In the cosolvent–[nonhydroxyl ILs] systems, a furcated H-bond was formed between the O atom of the cosolvent molecule and the C2-H and C6-H, while there were always H-bonds involving the OH group of the cation in the cosolvent–[hydroxyl ILs] systems. Introducing an OH group on the ethyl side of the imidazolium ring may change the order of solubility of the molecular liquids.     

Theoretical studies of structure, energetics and properties of Ca2+ complexes with alizarin glucoside

The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Density functional theory studies of interactions of polyphenol glycosides and Ca²⁺ were performed to determine preferred structures and the role of polyphenol and carbohydrate parts in the formation of complexes. The determination of these properties may be useful in designing new complexes, effectively interacting with calcium compounds. In the present study we try to define factors influencing interaction energies and stabilization. The determined structures were divided according to coordination numbers. Obtained data indicate that for stronger interactions complexes maximize the number of O-Ca²⁺ contacts.     

New dinuclear Co(II) and Mn(II) complexes of the phenol-based compartmental ligand containing formyl and amine functions: structural, spectroscopic and magnetic properties

The phenol-based compartmental ligand Hpy2ald contains a tridentate amino arm and a weak donor aldehyde group at the 2^′ and at the 6^′ positions of the phenol ring, respectively. This ligand reacts with cobalt(II) perchlorate, cobalt(II) tetrafluoroborate and manganese(II) perchlorate, yielding dinuclear complexes, where two metal ions are doubly bridged by two deprotonated cresolate moieties. The coordination environment around the metal ions is then completed to a very distorted octahedron by three nitrogen donor atoms from the pendant amino arm and the oxygen atom of the aldehyde group. The crystal structures of the complexes, their spectroscopic and magnetic properties are reported.     

Structure and electronic properties of heme complexes with various ligands

The electronic and atomic structures, and the molecular dynamics of the atomic structure at 310 K of a set of heme complexes with His and Gly amino acids in the 5th coordination position and some ligands (O2, NO) in the 6th position were studied by ab initio (3-21G basis set) and semiempirical (PM3) quantum chemistry methods and the method of molecular dynamics. It was shown that the type of coordination of the imidazole ring influences the constant of chemical bonding of molecular oxygen of the complexes. On the other hand, NO and O2 molecules have different transinfluence on the ligand in the 5th coordination position. It was shown that temperature affects profoundly the atomic and electronic structures of the complexes, the tightness of chemical bonding and their reactivity.     

Theoretical study of penta- and heteropentadienyl beryllium complexes coordinated to hydrogen molecules

A series of penta- and heteropentadienyl [CH₂CHCHCHXBe]⁺, (X?=?CH₂, O, NH, S) complexes has been theoretically studied. All calculated complexes show beryllium atoms with two, three, and five coordination numbers. The density functional theory (DFT) was used to determine the electron and structural behavior of those beryllium complexes. The nature of the ligands plays an important role in the form of binding to the beryllium atom. Beryllium structures 1–4 are able to coordinate only one hydrogen molecule. A molecular orbital analysis for all complexes was performed in order to know more about the nature of their bonding scheme.     

Crystal Structure of Organolanthanide Complexes [Li(THF)2]2 (μt-Cl)4(η5-C5 H5 )Ln·THF (Ln = La,Nd)

The crystal and molecular structures of the title compounds have been determined from single crystal X-ray diffraction. The two complexes crystallize in the orthorhombic space group Pna2₁ with Z = 4. Lattice parameters are: a = 10.504(2) [10.522(2)], ¹b = 16.816(4) [16.927(3)] and c = 18.931(4) [18.969(3)] Å. The two crystals are isomorphous. The structures were solved by Patterson and Fourier techniques and refined by least-squares techniques to R = 0.0430 for 1508 reflections. The Nd³⁺. ion is eight-coordinate, being bonded to five carbons of the cyclopentadiene ring, to four chloride atoms and to the one oxygen atom of the THF ring. The NdC distances are in the range 2.67–2.85 Å (average: 2.77 Å) and Nd-Cl distances are in the range 2.76–2.80 Å (average: 2.78 Å). The Nd-O distance is 2.52 A. The Li⁺ ion is four-coordinate, being bonded to the two chloride atoms and to the two oxygen atoms of the two THF rings. The other Li⁺ ion is the same as the above. The Li-Cl distances are in the range 2.17– 2.55 Å (average: 2.35 A) and LiO distances are in the range 1.89–1.98 Å (average: 1.91 Å). The Nd atom and the two Li atoms are bridged asymmetrically by the chloride ions, respectively.     

Adsorption and spin state properties of Cr,Ni, Mo,and Pt deposited on Li+ and Na+ monovalent cation impurities of MgO (001) surface: DFT calculations

We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg²⁺ site of a defect-free surface and at Li⁺ and Na⁺ sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal–support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg²⁺ site of the pure surface and at Li⁺ and Na⁺ sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to lanthanum and erbium ions

Lanthanide ions and erythritol form metal–alditol complexes with various structures. Lanthanum nitrate and erbium chloride coordinate to erythritol to give new coordination structures. The lanthanum nitrate–erythritol complex (LaEN), 2La(NO₃)₃·C₄H₁₀O₄·8H₂O, La³⁺ exhibits the coordination number of 11 (namely 11 polar atoms bound to one lanthanum) and is 11-coordinated to two hydroxyl groups from one erythritol molecule, six oxygen atoms from three nitrate ions and three water molecules. One erythritol molecule is coordinated to two La³⁺ ions and links the two metal ions together. The ratio of M:L is 2:1. The erbium chloride–erythritol complex (ErE), ErCl₂·C₄H₉O₄·2C₂H₅OH was obtained from ErCl₃ and erythritol in aqueous ethanol solution and the structure shows that deprotonation reaction occurs in the reaction process. The Er³⁺ cation is 8-coordinated with three hydroxyl groups of one erythritol molecule, two hydroxyl groups from another erythritol molecule, two ethanol molecules, and one chloride ion. Erythritol provides its three hydroxyl groups to one erbium cation and two hydroxyl groups to another erbium cation, that is, one hydroxyl group is coordinated to two metal ions and therefore loses its hydrogen atom and becomes a oxygen bridge. Another chloride ion is hydrogen bonded in the structure. The results indicate the complexity of metal–sugar coordination.     

A theoretical study of red-shifting and blue-shifting hydrogen bonds occurring between imidazolidine derivatives and PEG/PVP polymers

A theoretical study is presented with the aim to investigate the molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives. The substitution of the carbonyl groups for thiocarbonyl in the hydantoin scaffold was taken into account when analyzing the effect of the hydrogen bonds on imidazolidine derivatives. B3LYP/6-31G(d,p) calculations and topological integrations derived from the quantum theory of atoms in molecules (QTAIM) were applied with the purpose of examining the N–H⋯O hydrogen bond strengths formed between the amide group of the hydantoine ring and the oxygen atoms of PVP and PEG polymers. The effects caused by the N–H⋯O interaction fit the typical evidence for hydrogen bonds, which includes a variation in the stretch frequencies of the N–H bonds. These frequencies were identified as being vibrational red-shifts because their values decreased. Although the values of such calculated interaction energies are between 12 and 33 kJ mol⁻¹, secondary intermolecular interactions were also identified. One of these secondary interactions is formed through the interaction of the benzyl hydrogen atoms with the oxygen atoms of the PVP and PEG structures. As such, we have analyzed the stretch frequencies on the C–H bonds of the benzyl groups, and blue-shifts were identified on these bonds. In this sense, the intermolecular systems formed by hydantoine derivatives and PVP/PEG monomers were characterized as a mix of red-shifting and blue-shifting hydrogen-bonded complexes.     

Conserved Water Molecular Dynamics of the Different X-ray Structures of Rusticyanin: An Unique Aquation Potentiality of the Ligand Bonded Cu++ Center

Abstract

The invariant water molecular interaction involving in the Rusticyanin of Thiobacillus ferrooxidans is thought to be important for its molecular complexation with other proteins at differential acidophilic situation. The comparative analysis of the different x-ray, energy minimized, and auto solvated structures of Rusticyanin revealed the presence of five specific invariant bound water molecules (among the ~ 150 water molecules per monomer) in the crystals. The five W 205, W 206, W 112, W 214, and W 221 water molecules (in Rusticyanin PDB code: 1RCY) were seem to be invariant in all the seven structures (PDB codes: 1RCY, 1A3Z, 1A8Z, 1E3O, 1GY1, 1GY2, 2CAL). Among the five conserved water molecules the W 221 (of 1 RCY or the equivalent water molecules in the other oxidized form of Rusticyanin structures) had endowed an interesting coordination potentiality to Cu⁺² ion during the energy minimization. The W 221 was observed to approach toward the tetrahedrally bonded Cu⁺² ion through the opposite (or trans) route of metal-bonded Met 148. This direct water molecular coordination affected the tetrahedral geometry of Cu⁺² to trigonal bipyramidal. Presumably this structural dynamics at the Cu⁺² center could involve in the electron transport process during protein-protein complexation.     

Stability and solvation of alkali metal ion complexes with dibenzo-30-crown-10

Stability constants for the 1:1 complexes of dibenzo-30-crown-10 (DB30C10) with alkali metal ions have been determined at 25 °C in nitromethane and water by conductometry and capillary electrophoresis, respectively. Transfer activity coefficients of DB30C10 and its complexes from nitromethane to S (S = water, acetonitrile, propylene carbonate, methanol, and N,N-dimethylformamide) have been determined at 25 °C to evaluate the solvation properties. The stability constant in the poorly solvating solvent, nitromethane, decreases with increasing metal ion size, Na⁺ > K⁺ > Rb⁺ > Cs⁺, reflecting the intrinsic selectivity governed by electrostatic interaction between the metal ion and the ether oxygen atoms. It is also suggested that a part of the ether oxygen atoms does not bind to the metal ion in the Na(DB30C10)⁺ complex. The aqueous stability constant varies as Na⁺ ? K⁺ ≈ Rb⁺ ≈ Cs⁺; this selectivity pattern is similar to that in acetonitrile, propylene carbonate, and methanol. The complex stability in water is very low compared to that in the nonaqueous solvents, owing to hydrogen bonding of water to the oxygen atoms of the free crown ether. The transfer activity coefficient values show that DB30C10 shields all the metal ions effectively from the solvents and lead to the conclusion that the complexation selectivity in S receives a significant contribution from the solvation of the free metal ions. The Na(DB30C10)⁺ complex has specific interaction with water, causing much lower K⁺/Na⁺ selectivity in H₂O than in MeOH.