Ab initio and density functional theoretical design and screening of model crown ether based ligand (host) for extraction of lithium metal ion (guest): effect of donor and electronic induction

The structures, energetic and thermodynamic parameters of model crown ethers with different donor, cavity and electron donating/ withdrawing functional group have been determined with ab initio MP2 and density functional theory in gas and solvent phase. The calculated values of binding energy/ enthalpy for lithium ion complexation are marginally higher for hard donor based aza and oxa crown compared to soft donor based thia and phospha crown. The calculated values of binding enthalpy for lithium metal ion with 12C4 at MP2 level of theory is in good agreement with the available experimental result. The binding energy is altered due to the inductive effect imparted by the electron donating/ withdrawing group in crown ether, which is well correlated with the values of electron transfer. The role of entropy for extraction of hydrated lithium metal ion by different donor and functional group based ligand has been demonstrated. The HOMO-LUMO gap is decreased and dipole moment of the ligand is increased from gas phase to organic phase because of the dielectric constant of the solvent. The gas phase binding energy is reduced in solvent phase as the solvent molecules weaken the metal-ligand binding. The theoretical values of extraction energy for LiCl salt from aqueous solution in different organic solvent is validated by the experimental trend. The study presented here should contribute to the design of model host ligand and screening of solvent for metal ion recognition and thus can contribute in planning the experiments.     

The macrocyclic and cryptate effect. 4. Complexation of cobalt(II) and nickel(II) by noncyclic,monocyclic and bicyclic ligands in methanol

The complex formation of Co²⁺ and Ni²⁺ with various noncyclic ligands, aza crown ethers and cryptands has been studied in methanol by means of calorimetric and potentiometric titrations. The reactions of both cations with aza crown ethers were endothermic. This surprising result can be explained by structural changes of the ligand during the complexation process. The thermograms for the titration of Ni²⁺ solutions with cryptands show two different reactions. On the basis of further results from potentiometric titrations, a two-step reaction mechanism is discussed. The macrocyclic and the cryptate effect are only caused by favourable entropic changes.     

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.     

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.     

Synthesis, DNA cleavage, and cytotoxicity of a series of bis(propargylic) sulfone crown ethers

Compounds that couple molecular recognition of specific alkali metal ions with DNA damage may display selective cleavage of DNA under conditions of elevated alkali metal ion levels reported to exist in certain cancer cells. We have prepared a homologous series of compounds in which a DNA reactive moiety, a bis(propargylic) sulfone, is incorporated into an alkali metal ion binding crown ether ring. Using the alkali metal ion pricrate extraction assay, the ability of these crown ethers to bind Li(+), Na(+), and K(+) ions was determined. For the series of crown ethers, the association constants for Li(+) ions are generally low (< 2 x 10(4)M(-1)). Only two of the bis(propargylic) sulfone crown ethers associate with Na(+) or K(+) ions (K(a) 4-8 x 10(4)M(-1)), with little discrimination between Na(+) or K(+) ions. The ability of these compounds to cleave supercoiled DNA at pH 7.4 in the presence of Li(+), Na(+), and K(+) ions was determined. The two crown ethers that bind Na(+) and K(+) display a modest increase in DNA cleavage efficiency in the presence of Na(+) or K(+) ions as compared to Li(+) ions. These two bis(propargylic) sulfone crown ethers are also more cytotoxic against a panel of human cancer cell lines when compared to a non-crown ether macrocyclic bis(propargylic) sulfone.     

Effect of membrane association on the stability of complexes between ionophore A23187 and monovalent cations

The monovalent cation complexation properties of ionophore A23187 in methanol-water (65-95% w/w) and bound to unilamellar vesicles of dimyristoylphosphatidylcholine (DMPC) are contrasted. In both solution and vesicle-containing systems, 1:1 complexes between the ionophore and Li+ or Na+ predominate. The analogous complexes with K+, Rb+, and Cs+, which exist in methanol, are not detected on DMPC vesicles by changes in the absorption or fluorescence emission spectra of the ionophore. In solution, the logarithms of stability constants (log KMA) for both the LiA and NaA complexes increase by 1.5 units over the range of solvent polarity encompassed by 65% methanol-water to methanol. Selectivity for Li+ vs. Na+ is constant at a ratio of 5 in these solutions. On DMPC vesicles, selectivity for Li+ vs. Na+ is improved 15-fold with log KbLiA (3.23 +/- 0.03, T = 25 degrees C, mu = 0.05 M) being comparable to the value obtained in 80% methanol-water. In the latter solvent, increasing ionic strength (0.005-0.085 M) has little effect on log KLiA or log KHA but increases these constants by 0.4-0.5 unit in the DMPC vesicle system. Transition from the vesicle liquid-crystalline to gel-phase state reduces log KbLiA and log KbNaA by approximately 0.6 unit but has no effect on log KbHA. Thermodynamic parameters for formation of HA, LiA, and NaA in 80% methanol-water and on DMPC vesicles are reported. Analysis of these data and related considerations suggests that differences in the membrane interaction energies of particular ionophore species dominate in establishing the observed difference in complexation properties between the solution and vesicle-containing systems.     

Deuterium solvent isotope effect and proton-inventory studies of factor Xa-catalyzed reactions

Kinetic solvent isotope effects (KSIEs) for the factor Xa (FXa)-catalyzed activation of prothrombin in the presence and absence of factor Va (FVa) and 5.0 x 10(-5) M phospholipid vesicles are slightly inverse, 0.82-0.93, when substrate concentrations are at 0.2 Km. This is consistent with the rate-determining association of the enzyme-prothrombin assembly, rather than the rate-limiting chemical transformation. FVa is known to effect a major conformational change to expose the first scissile bond in prothrombin, which is the likely event triggering a major solvent rearrangement. At prothrombin concentrations > 5 Km, the KSIE is 1.6 +/- 0.3, when FXa is in a 1:1 ratio with FVa but becomes increasingly inverse, 0.30 +/- 0.05 and 0.19 +/- 0.04, when FXa/FVa is 1:4, with an increasing FXa and substrate concentration. The rate-determining step changes with the conditions, but the chemical step is not limiting under any circumstance. This corroborates the proposed predominance of the meizothrombin pathway when FXa is well-saturated with the prothrombin complex. In contrast, the FXa-catalyzed hydrolysis of N-alpha-Z-D-Arg-Gly-Arg-pNA.2HCl (S-2765) and H-D-Ile-L-Pro-L-Arg-pNA.HCl (S-2288) is most consistent with two-proton bridges forming at the transition state between Ser195 OgammaH and His57 N(epsilon)2 and His57 Ndelta1 and Asp102 COObeta- at the active site, with transition-state fractionation factors of phi1 = phi2 = 0.57 +/- 0.07 and phiS = 0.78 +/- 0.16 for solvent rearrangement for S-2765 and phi1 = phi2 = 0.674 +/- 0.001 for S-2288 under enzyme saturation with the substrate at pH 8.40 and 25.0 +/- 0.1 degrees C. The rate-determining step(s) in these reactions is most likely the cleavage of the C-N bond and departure of the leaving group.     

Homoleptic platinum(II) and palladium(II) complexes of 1,5,9-trithiacyclododecane: the crystal structures of [Pt(12S3)2](PF6)2 · 2CH3NO2 and [Pd(12S3)2](BF4)2 · 0.5H2O

The synthesis, spectroscopy, electrochemistry, and crystal structures of two new mononuclear homoleptic Pt(II) and Pd(II) complexes with the crown trithioether 1,5,9-trithiacyclododecane (12S3) are reported. In contrast to behavior with analogous smaller ring trithiacrowns, both metal complexes exhibit exodentate axial sulfur donors, a consequence of the preferred conformation of the 12S3 ligand. The lack of two axial metal-sulfur interactions correlates with the observed electronic spectroscopy and oxidative electrochemistry displayed by the complexes and contrasts with properties exhibited by complexes containing smaller polythioether macrocycles. The two complexes have electronic spectra dominated by charge transfer, not d-d bands and show no M²⁺/M³⁺ couples. Both complexes show a fluxional 12S3 ligand in solution due to a 1,5-metallotropic shift, an uncommon observation of this particular type of intramolecular ligand exchange. The ¹⁹⁵Pt NMR chemical shift of −4201 ppm for [Pt(12S3)₂]²⁺ is consistent with an alternating positioning of the four sulfur lone pairs on the coordinated thioethers. Although 12S3 is poorly pre-organized for facial complexation, its flexibility to position a sulfur in an exodentate fashion enables it to form stable complexes with d⁸ metal ions such as Pt(II) and Pd(II).     

Sodium ions and an energized membrane required by Methanosarcina barkeri for the oxidation of methanol to the level of formaldehyde.

Methanogenesis from methanol by cell suspensions of Methanosarcina barkeri was inhibited by the uncoupler tetrachlorosalicylanilide. This inhibition was reversed by the addition of formaldehyde. 14C labeling experiments revealed that methanol served exclusively as the electron acceptor, whereas formaldehyde was mainly oxidized to CO2 under these conditions. These data support the hypothesis (M. Blaut and G. Gottschalk, Eur. J. Biochem. 141: 217-222, 1984) that the first step in methanol oxidation depends on the proton motive force or a product thereof. Cell extracts of M. barkeri converted methanol and formaldehyde to methane under an H2 atmosphere. Under an N2 atmosphere, however, formaldehyde was disproportionated to CH4 and CO2, whereas methanol was metabolized to a very small extent only, irrespective of the presence of ATP. It was concluded that cell extracts of M. barkeri are not able to oxidize methanol. In further experiments, the sodium dependence of methanogenesis and ATP formation by whole cells was investigated. Methane formation from methanol alone and the corresponding increase in the intracellular ATP content were strictly dependent on Na+. If, in contrast, methanol was utilized together with H2, methane and ATP were synthesized in the absence of Na+. The same is true for the disproportionation of formaldehyde to methane and carbon dioxide. From these experiments, it is concluded that in M. barkeri, Na+ is involved not in the process of ATP synthesis but in the first step of methanol oxidation.     

Synthesis, spectroscopic, structural and complexation studies of a new tetra-naphthylmethylene pendant-armed macrocyclic ligand

A novel emissive tetra-naphthylmethylene pendant-armed macrocyclic ligand and a series of complexes with monovalent and divalent metal ions have been synthesized. Solid compounds have been isolated as mononuclear (Co(II), Cu(II) and Zn(II)) or dinuclear (Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Ag(I)), complexes, depending on the counterions used. The chemical and photophysical properties of the free ligand, the protonation behavior and its metal complexes have been investigated in solution. UV-Vis spectroscopy has revealed a 1:1 binding stoichiometry for Cu(II), Zn(II), Cd(II), Ni(II) and Co(II), and 2:1 molar ratio for Ag(I). In chloroform, the free ligand presents two emission bands related to the monomer naphthalene emission and a red-shifted band attibutable to an exciplex due to a charge transfer from the nitrogen lone electron pair to the excited chromophore. Upon protonation of the free amines or due to metal complexation, the exciplex band disappears. The crystal structure of [Ag₂L(NO₃)₂] is also reported. The structure reveals that both metal ions are into the macrocyclic cavity in a distorted square plane {AgN₃O} environment. Each Ag(I) atom interacts with two neighbouring amine nitrogen atoms, one pyridine nitrogen and one oxygen atom from a monodentate nitrate ion.     

Mechanism of the cobalt-catalyzed carbonylation of ethyl diazoacetate

Carbonyl cobalt complexes serve as catalysts or catalyst precursors for the facile and selective transformation of primary diazoalkanes into the corresponding ketene. The mechanism of this carbonylation reaction has been elucidated in the case of ethyl diazoacetate as model diazoalkane using octacarbonyl dicobalt as the catalyst precursor. Dinuclear cobalt complexes having ethoxycarbonylcarbene ligand(s) in bridging position(s) have been identified as active intermediary of the catalytic cycles and their relevant chemical properties have been explored. Key step of the carbonylation is the formation of the highly reactive ethoxycarbonylketene by intramolecular coupling of a carbonyl ligand with the ethoxycarbonylcarbene ligand. DFT calculations reveal that the ketene formation takes place via a rapid coupling of the carbene ligand with one terminal CO followed by coordination of an external carbon monoxide and by a facile intramolecular rearrangement and ketene elimination. The ethoxycarbonylketene can be in situ trapped by OH, NH, or CH acid compounds or by N-substituted imines. In the presence of ethanol diethyl malonate is the only product of the catalytic carbonylation of ethyl diazoacetate. On the bases of the kinetics of the composing steps of the catalytic cycles, localization of the rate-determining step(s) under various reaction conditions has been made.     

Why do crown ethers activate enzymes in organic solvents?

One of the major drawbacks of enzymes in nonaqueous solvents is that their activity is often dramatically low compared to that in water. This limitation can be largely overcome by crown ether treatment of enzymes. In this paper, we describe a number of carefully designed new experiments that have improved the insights into the mechanisms that are operative in the crown ether activation of enzymes in organic solvents. The enhancement of enzyme activity upon addition of 18-crown-6 to the organic solvent can be reconciled with a mechanism in which macrocyclic interactions of 18-crown-6 with the enzyme play an important role. Macrocyclic interactions (e.g., complexation with lysine ammonium groups of the enzyme) can lead to a reduced formation of inter- and intramolecular salt bridges and, consequently, to lowering of the kinetic conformational barriers, enabling the enzyme to refold into thermodynamically stable, catalytically (more) active conformations. This assumption is supported by the observation that the crown-ether-enhanced enzyme activity is retained after removal of the crown by washing with a dry organic solvent. A much stronger crown ether activation is observed when 18-crown-6 is added prior to lyophilization, and this can be explained by a combination of two effects: the before-mentioned macrocyclic complexation effect, and a less specific, nonmacrocyclic, lyoprotecting effect. The magnitude of the total crown ether effect depends on the polarity and thermodynamic water activity of the solvent, the activation being highest in dry and apolar media, where kinetic conformational barriers are highest. By determination of the specific activity of crown-ether-lyophilized enzyme as a function of the enzyme concentration, the macrocyclic crown ether (linearly dependent on the enzyme concentration) and the nonmacrocyclic lyoprotection effect (not dependent on the enzyme concentration) could be separated. These measurements reveal that the contribution of the nonmacrocyclic effect is significantly larger than the macrocyclic refolding effect.     

Catalytic cycle of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus. Solvent viscosity, deuterium isotope effects, and proton inventory studies

The phosphatidylcholine-preferring phospholipase C from Bacillus cereus (PLCBc) is a 28.5 kDa enzyme with three zinc ions in its active site. Although much is known about the roles that various PLCBc active site amino acids play in binding and catalysis, there is little information about the rate-determining step of the PLCBc-catalyzed hydrolysis of phospholipids and the catalytic cycle of the enzyme. To gain insight into these aspects of the hydrolysis, solvent viscosity variation experiments were conducted to determine whether an external step (substrate binding or product release) or an internal step (hydrolysis) is rate-limiting. The data indicate that the PLCBc-catalyzed reaction is unaffected by changes in solvent viscosity. This observation is inconsistent with the notion of substrate binding or product release being rate-determining and supports the hypothesis that a chemical step is rate-limiting. Furthermore, a deuterium isotope effect of 1.9 and a linear proton inventory plot indicate one proton is transferred in the rate-determining step. These data may be used to formulate a comprehensive catalytic cycle that is for the first time based on experimental evidence. In this mechanism, Asp55 of PLCBc activates an active site water molecule for attack on the phosphodiester bond, the hydrolysis of which is rate-limiting. The phosphorylcholine product is the first to leave the active site, followed by diacylglycerol.     

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.     

Novel crown ethers on glucose based glycolipids

A series of crown ethers involving lauryl glucoside were synthesized and their assembly behavior in water was studied. The synthesis applied a simple protection scheme based on benzylidenation for the glycolipid, and cation templating for the macrocycle. A sequential build-up of the crown ether by bis-hydroxylethylation of the glucoside followed by reaction with di-, tri-, or tetraethylene glycol ditosylate provided better yields of the macrocycle compared to a single step cyclization with tetraethylene glycole ditosylate. The macrocycles containing up to six oxygens showed significantly higher affinity for sodium than for potassium, while more effective potassium complexation was found for the 21-crown-7 compound. The ion binding affinity leads to a slight but significant increase of the CMC of the crown ether containing surfactant in water upon the addition of sodium electrolyte.     

The macrocyclic and cryptate effect. 7. Influence of structural changes on the complexation behaviour of aza crown ethers and cryptands in different solvents

The complex formation of several mono- and bivalent cations with aza crown ethers, cryptands, and the dilactam analogues of both ligands has been studied in methanol and acetonitrile by means of calorimetric and potentiometric titrations. The complex stabilities of the dilactam ligands are reduced by a factor of more than 10⁶ compared with the unsubstituted ligands. This decrease is mainly caused by a strong reduction in the values of the reaction enthalpies. The variation of the mono- and bicyclic ligand structures causes a complete loss of the macrocyclic and cryptate effect.     

Cryoenzymology of the hammerhead ribozyme.

The technique of cryoenzymology has been applied to the hammerhead ribozyme in an attempt to uncover a structural rearrangement step prior to cleavage. Several cryosolvents were tested and 40% (v/v) methanol in water was found to perturb the system only minimally. This solvent allowed the measurement of ribozyme activity between 30 and -33 degrees C. Eyring plots are linear down to -27 degrees C, but a drastic reduction in activity occurs below this temperature. However, even at extremely low temperatures, the rate is still quite pH dependent, suggesting that the chemical step rather than a structural rearrangement is still rate-limiting. The nonlinearity of the Eyring plot may be the result of a transition to a cold-denatured state or a glassed state.     

Density functional theory analysis of carbonyl sulfide hydrolysis: effect of solvation and nucleophile variation

The detailed mechanisms of the hydrolysis of carbonyl sulfide (OCS) by nucleophilic water and hydroxide ion in both the gas phase and bulk water solvent have been investigated using density functional theory. Various reaction channels on the potential surface have been identified. The thermodynamic results demonstrate that the hydrolysis of OCS by nucleophilic water and hydroxide ion should proceed more favorably at low temperature. The hydrolysis of OCS by the hydroxide ion is the main reaction channel from thermodynamic and kinetic perspectives, and the bulk solvent can influence the rate-determining step in this channel. However, the solvent barely modifies the activation energy of the rate-determining step. For the hydrolysis of OCS by nucleophilic water, the solvent does not modify the rate-determining step, and the corresponding activation energy of the rate-determining step barely changes. This bulk solvent effect suggests that most of the contribution of the solvent is accounted for by considering one water molecule and a hydroxide ion.     

Catalytic activity of iron phthalocyanine for the oxidation of thiocyanate and L-cysteine anchored on Au(111) clusters

ABSTRACT

We studied the oxidation reactions of thiocyanate and L-cysteine on iron phthalocyanine (FePc) coupled via a bridging ligand of the 4-mercatopyridine (4MP) type to a gold cluster (Au₂₆), aiming to simulate a modified gold electrode. Theoretical models have been used based on the framework of density functional theory. Several mechanistic pathways are explored for the study of these reactions, finding that the most favorable mechanism involves an electron transfer process as the rate-determining step. Along the process, the ability of the gold cluster to act as an electron acceptor facilitating the reactions was detected. In addition, the proposed models presented a correlation between the energy obtained for the rate-determining step of the reaction and the experimental oxidation potentials of the thiocyanate and L-cysteine.     

Reaction between iron(III) and pyrazoic acid

In the reaction of [Fe(H₂O)₆]³⁺ with pyrazoic acid, reduction of iron(III) to iron(II) is observed. When an excess of iron is present, the reaction involves a transfer of four electrons per mole of acid. At room temperature the redox reaction, which is dependent on hydrogen ion, iron(III) and pyrazoic acid concentrations, is rather slow and is the rate-determining step. The kinetic study was carried out at 50.0 ± 0.1 °C. The redox reaction is followed by a fast reaction of the iron(II) with an excess of ligand, resulting in the production of well-known complexes, where the acid acts as a chelating ligand through the nitrogen and oxygen atoms.