Efficient Molecular Catalysis of ATP-Hydrolysis by Protonated Macrocyclic Polyamines

Molecular catalysis of ATP-hydrolysis by a number of protonated macrocyclic polyamines 1–9 has been investigated by ³¹P-NMR spectroscopy, and marked rate enhancements have been obtained. The largest acceleration is produced by the [24]-N₆O₂ macrocycle 1 , and the process displays the following properties: 1. protonated 1 forms very stable complexes with ATP, as well as with ADP and AMP; 2. it enhances the rate of ATP-hydrolysis by a factor of 10³ at pH = 8.5; the rate of hydrolysis is constant over a wide pH-range, from pH = 2.5 to 8.5; 3. 1 is more efficient than acyclic analogues; 4. the products of the reaction are orthophosphate (OP) and ADP, which is subsequently hydrolyzed to OP and AMP at a slower rate; 5. at pH > 6.5, a transient species is detected, which is tentatively identified as a phosphoramidate intermediate, resulting from phosphorylation of the macrocycle 1 ; 6. the reaction presents first-order kinetics and is catalytic. The mechanism of the process is discussed in terms of initial formation of a complex between ATP and protonated 1 , followed by an intracomplex reaction which may involve a combination of nucleophilic or acid catalysis with electrostatic catalysis.     

Infrared spectroscopic study of the protonated ligand salts of a 15-membered dioxa-diaza macrocycle

The 15-membered mixed dioxa-diaza macrocycle 5,6,14,15-dibenzo-1,4-dioxa-8,12-diazacyclopentadeca-5,14-diene (L) by reactions with a series of sodium salts NaX (X = picrate, ClO₄, BF₄, PF₆ and BPh₄) in acetonitrile and methanol solution yielded the protonated macrocyclic salts with different proton-to-ligand ratio as well as different modes of inside and outside macrocycle protonation and hydrogen bonding systems. Infrared spectra of the ion-pair compounds [H(L)]X with intraligand protonation as well as [H(L)₂]X and [H₂(L)₃](X)₂ with interligand protonation, have been studied. The results obtained are discussed with respect to reported X-ray structure data of these compounds.     

Reactions of (Hydroxo)aluminium(III)tetra(4-chloro)phthalocyanine in Sulfuric Acid

Spectrophotometric and quantum-chemical data showed that (hydroxo)aluminium(III)tetra(4-chloro)phthalocyanine forms one protonated form (trans-dication) in aqueous concentrated H₂SO₄. The kinetics of the protonated complex dissociation across the Al–N bonds is studied. The effect of the halogen substitution in the aluminium phthalocyanine macrocycle on its basicity and stability is discussed.     

Oxazolone versus macrocycle structures for leu-enkephalin b<Subscript>2</Subscript>–b<Subscript>4</Subscript>: Insights from infrared multiple-photon dissociation spectroscopy and gas-phase hydrogen/deuterium exchange

The collision-induced dissociation (CID) products b₂-b₄ from Leu-enkephalin are examined with infrared multiple-photon dissociation (IR-MPD) spectroscopy and gas-phase hydrogen/deuterium exchange (HDX). Infrared spectroscopy reveals that b₂ exclusively adopts oxazolone structures, protonated at the N-terminus and at the oxazolone ring N, based on the presence and absence of diagnostic infrared vibrations. This is correlated with the presence of a single HDX rate. For the larger b₃ and b₄, the IR-MPD measurements display diagnostic bands compatible with a mixture of oxazolone and macrocycle structures. This result is supported by HDX experiments, which show a bimodal distribution in the HDX spectra and two distinct rates in the HDX kinetic fitting. The kinetic fitting of the HDX data is employed to derive the relative abundances of macrocycle and oxazolone structures for b₃ and b₄, using a procedure recently implemented by our group for a series of oligoglycine b fragments (Chen et al. J. Am. Chem. Soc. 2009, 131(51), 18272–18282. doi: 10.1021/ja9030837). In analogy to that study, the results suggest that the relative abundance of the macrocycle structure increases as a function of b fragment size, going from 0% for b₂ to ∼6% for b₃, and culminating in 31% for b₄. Nonetheless, there are also surprising differences between both studies, both in the exchange kinetics and the propensity in forming macrocycle structures. This indicates that the chemistry of “head-to-tail” cyclization depends on subtle differences in the sequence as well as the size of the b fragment.     

Metal complexes with macrocyclic ligands. Part XXXIV. Geometrical and conformational changes during the on/off reaction of the side chain in the CuII complex of 11-(3-aminopropyl)-1,4,7,11-tetraazacyclotetradecane

Solution studies of the Cu²⁺ complex with 11-(3-aminopropyl)-1,4,7,11-tetraazacyclotetradecane(L) indicate that, depending on the pH and on the age of the solution, different species are present. Dissolving the solid [CuL](ClO₄)₂ in slightly acidic solution gives the protonated complex AH , characterized by an absorption maximum at 574 nm, by a relatively fast proton-induced dissociation kinetics and by the typical colour change in basic solution to give the deprolonated form A with coordinated side chain. AH slowly interconverts in acidic solution to a new species BH , which has an absorption maximum at 547 nm, and which is kineticaily more stable against acid dissociation and shows no coordination of the amino group of the side chain. In alkaline solution, however, the deprotonated form B deliver A in a base induced reaction. The X-ray diffraction studies of A and BH allow to determine the geometry of the metal ion and the configuration of the macrocycle. In A , the Cu²⁺ is pentacoordinated by the five N-atoms of the ligand and the macrocycle is in the RRSR configuration, whereas in BH the Cu²⁺ is octahedrally coordinated by the four N-atoms of the macrocycle and two axial perchlorate O-atoms with the macrocycle in the RRRS configuration. The amino group of the side chain is protonated and not coordinated. Thus, the on/off equilibrium of the side chain not only changes the geometry of the metal ion, as is generally found, but also alters the macrocyclic moiety.     

Siamese‐Twin Porphyrin: A Pyrazole‐Based Expanded Porphyrin of Persistent Helical Conformation

The 3+3‐type synthesis of a pyrazole‐based expanded porphyrin 22 H₄ , a hexaphyrin analogue named Siamese‐twin porphyrin, and its homobimetallic diamagnetic nickel(II) and paramagnetic copper(II) complexes, 22 Ni₂ and 22 Cu₂ , are described. The structure of the macrocycle composed of four pyrroles and two pyrazoles all linked by single carbon atoms, can be interpreted as two conjoined porphyrin‐like subunits, with the two opposing pyrazoles acting as the fusion points. Variable‐temperature 1D and 2D NMR spectroscopic analyses suggested a conformationally flexible structure for 22 H₄ . NMR and UV/Vis spectroscopic evidence as well as structural parameters proved the macrocycle to be non‐aromatic, though each half of the molecule is fully conjugated. UV/Vis and NMR spectroscopic titrations of the free base macrocycle with acid showed it to be dibasic. In the complexes, each metal ion is coordinated in a square‐planar fashion by a dianionic, porphyrin‐like {N₄} binding pocket. The solid‐state structures of the dication and both metal complexes were elucidated by single‐crystal diffractometry. The conformations of the three structures are all similar to each other and strongly twisted, rendering the molecules chiral. The persistent helical twist in the protonated form of the free base and in both metal complexes permitted resolution of these enantiomeric helimers by HPLC on a chiral phase. The absolute stereostructures of 22 H₆ ²⁺, 22 Ni₂ , and 22 Cu₂ were assigned by a combination of experimental electronic circular dichroism (ECD) investigations and quantum‐chemical ECD calculations. The synthesis of the first member of this long‐sought class of expanded porphyrin‐like macrocycles lays the foundation for the study of the interactions of the metal centers within their bimetallic complexes.     

Highly effective electrochemical anion sensing based on oxoporphyrinogen

The effect of anion binding on the oxidation potential of an anion receptor, N₂₁,N₂₃-dibenzyl-5,10,15,20-(3,5-di-t-butyl-4-oxo-cyclohexa-2,5-dienylidene)porphyrinogen, 1 in o-dichlorobenzene is reported. The anion binding site of 1, at its inner pyrrolic amine hydrogens, is an integral part of the highly conjugated macrocycle, thus predicting larger potential shifts upon anion binding. Accordingly, cathodic shifts up to 600 mV are observed upon anion binding and such potential shifts correlate well with the anion binding constants.     

Gas-phase fragmentation of long-lived cysteine radical cations formed via no loss from protonated S-nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys^•+), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: •COOH ≫ CH₂S > •CH₂SH-H₂S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys^•+ with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH₂S, •COOH, •CH₂SH, and H₂S.     

CB‐TE2A+·Cl−·3H2O: a short intermolecular hydrogen bond between zwitterionic bicyclo[6.6.2]tetraamine macrocycles

1,4,8,11‐Tetraazabicyclo[6.6.2]hexadecane‐4,11‐diacetic acid (CB‐TE2A) is of much interest in nuclear medicine for its ability to form copper complexes that are kinetically inert, which is beneficial in vivo to minimize the loss of radioactive copper. The structural chemistry of the hydrated HCl salt of CB‐TE2A, namely 11‐carboxymethyl‐1,8‐tetraaza‐4,11‐diazoniabicyclo[6.6.2]hexadecane‐4‐acetate chloride trihydrate, C₁₆H₃₁N₄O₄⁺·Cl⁻·3H₂O, is described. The compound crystallized as a positively charged zwitterion with a chloride counter‐ion. Two of the amine groups in the macrocyclic ring are protonated. Formally, a single negative charge is shared between two of the carboxylic acid groups, while one chloride ion balances the charge. Two intramolecular hydrogen bonds are observed between adjacent pairs of N atoms of the macrocycle. Two intramolecular hydrogen bonds are also observed between the protonated amine groups and the pendant carboxylate groups. A short intermolecular hydrogen bond is observed between two partially negatively charged O atoms on adjacent macrocycles. The result is a one‐dimensional polymeric zigzag chain that propagates parallel to the crystallographic a direction. A second intermolecular interaction is a hydrogen‐bonding network in the crystallographic b direction. The carbonyl group of one macrocycle is connected through the three water molecules of hydration to the carbonyl group of another macrocycle.     

Effects of Alkali Metal Ion Cationization on Fragmentation Pathways of Triazole-Epothilone

The collisionally activated dissociation mass spectra of the protonated and alkali metal cationized ions of a triazole-epothilone analogue were studied in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation pathway of the protonated ion was characterized by the loss of the unit of C₃H₄O₃. However, another fragmentation pathway with the loss of C₃H₂O₂ was identified for the complex ions with Na⁺, K⁺, Rb⁺, and Cs⁺. The branching ratio of the second pathway increases with the increment of the size of alkali metal ions. Theoretical calculations based on density functional theory (DFT) method show the difference in the binding position of the proton and the metal ions. With the increase of the radii of the metal ions, progressive changes in the macrocycle of the compound are induced, which cause the corresponding change in their fragmentation pathways. It has also been found that the interaction energy between the compound and the metal ion decreases with increase in the size of the latter. This is consistent with the experimental results, which show that cesiated complexes readily eject Cs⁺ when subject to collisions.     

Synthesis of all optically active spermine macrocycle, (S)-6-(hydroxymethyl)-1,5,10,14-tetraazacyclooctadecane,and its complexation to ATP

The title compound was prepared in high yield from L-ornithine via a Richman-Atkins type macrocyclization. ³¹P-NMR binding studies indicate formation of a 1:1 complex of the protonated macrocycle with ATP.     

Switchable dual binding mode molecular shuttle

[Structure: see text] Protonation controls the location of a dual binding mode macrocycle in a [2]rotaxane. In the neutral form, amide-amide hydrogen bonds hold the macrocycle over a dipeptide residue; when the thread is protonated, polyether-ammonium cation interactions dominate and the macrocycle changes position.     

Axial ligand influence on geometries, charge distributions and electronic structures of iron tetraazamacrocycle [FeTIM(X)(Y)] complexes assessed by Density Functional Theory

We employed the Density Functional Theory along with small basis sets, B3LYP/LANL2DZ, for the study of FeTIM complexes with different pairs of axial ligands (CO, H₂O, NH₃, imidazole and CH₃CN). These calculations did not result in relevant changes of molecular quantities as bond lengths, vibrational frequencies and electronic populations supporting any significant back-donation to the carbonyl or acetonitrile axial ligands. Moreover, a back-donation mechanism to the macrocycle cannot be used to explain the observed changes in molecular properties along these complexes with CO or CH₃CN. This work also indicates that complexes with CO show smaller binding energies and are less stable than complexes with CH₃CN. Further, the electronic band with the largest intensity in the visible region (or close to this region) is associated to the transition from an occupied 3d orbital on iron to an empty π^∗ orbital located at the macrocycle. The energy of this Metal-to-Ligand Charge Transfer (MLCT) transition shows a linear relation to the total charge of the macrocycle in these complexes as given by Mulliken or Natural Population Analysis (NPA) formalisms. Finally, the macrocycle total charge seems to be influenced by the field induced by the axial ligands.     

Diagnostic NH and OH Vibrations for Oxazolone and Diketopiperazine Structures: b<Subscript>2</Subscript> from Protonated Triglycine

We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b₂ from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H⁺ stretch of the protonated carbonyl group at 3585 cm^–1. Conversely, b₂ from protonated triglycine exhibits a strong band at 3345 cm^–1, associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH₂ and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.     

DFT calculation of benzoazacrown ethers and their complexes with calcium perchlorate

The complexation constants of several azacrown ethers with Ca(ClO₄)₂ were determined and turned out to be the higher, the large the macrocycle. The structures of free ligands and their complexes and the complexation energies were calculated by the DFT method. In the aza-12(15)-crown-4(5) ether complexes with Ca(ClO₄)₂, the metal cations lie outside the averaged plane of heteroatoms of the macrocycle, and the coordination of both counterions is V-like. In the complexes of aza-18-crown-6 ethers, the counterions are in the axial position relatively to the macrocycle in the center of which the Ca²⁺ ion is localized. The complexation energies increase with an increase in the size of the azacrown ether macrocycle. The involvement of the nitrogen atom in binding with the Ca²⁺ ion decreases with the expansion of the macrocycle. Two methods for quantitative estimation of the degree of pre-organization of ligands to complexation were considered: geometric and energetic methods. Benzoaza-15-crown-5 ether is a ligand which is more pre-organized to complexation than N-phenylaza-15-crown-5 ether.     

Complexation Between (O‐Methyl)6‐2,6‐Helic[6]arene and Tertiary Ammonium Salts: Acid/Base‐ or Chloride‐Ion‐Responsive Host–Guest Systems and Synthesis of [2]Rotaxane

Complexation between (O ‐methyl)₆‐2,6‐helic[6]arene and a series of tertiary ammonium salts was described. It was found that the macrocycle could form stable complexes with the tested aromatic and aliphatic tertiary ammonium salts, which were evidenced by ¹H NMR spectra, ESI mass spectra, and DFT calculations. In particular, the binding and release process of the guests in the complexes could be efficiently controlled by acid/base or chloride ions, which represents the first acid/base‐ and chloride‐ion‐responsive host–guest systems based on macrocyclic arenes and protonated tertiary ammonium salts. Moreover, the first 2,6‐helic[6]arene‐based [2]rotaxane was also synthesized from the condensation between the host–guest complex and isocyanate.     

Enzymatic and catalytic reduction of dinitrogen to ammonia: Density functional theory characterization of alternative molybdenum active sites

We used density functional calculations to model dinitrogen reduction by a FeMo cofactor containing a central nitrogen atom and by a Mo‐based catalyst. Plausible intermediates, reaction pathways, and relative energetics in the enzymatic and catalytic reduction of N₂ to ammonia at a single Mo center are explored. Calculations indicate that the binding of N₂ to the Mo atom and the subsequent multiple proton–electron transfer to dinitrogen and its protonated species involved in the conversion of N₂ are feasible energetically. In the reduction of N₂ the Mo atom experiences a cycled oxidation state from Mo(IV) to Mo(VI) by nitrogenase and from Mo(III) to Mo(VI) by the molybdenum catalyst, respectively, tuning the gradual reduction of N₂. Such a wide range of oxidation states exhibited by the Mo center is crucial for the gradual reduction process via successive proton–electron transfer. Present results suggest that the Mo atom in the N‐centered FeMo cofactor is a likely alternative active site for dinitrogen binding and reduction under mild conditions once there is an empty site available at the Mo site. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Metal Complexes with Macrocyclic Ligands. Part XLI. Nickel(II) and copper(II) complexes with mono-N-functionalized dithiadiazamacrocycles

Three N₂S₂ macrocycles ( 3, 10, 12 ) carrying an amino group as a pendant arm have been synthesized and their complexation properties towards Ni²⁺ and Cu²⁺ studied. The crystal structures of the Cu²⁺ complexes with 10-methyl-1,4-dithia-7,10-diazacyclododecane-7-ethanamine ( 3 ) and 11-methyl-1,4-dithia-8,11-diazacyclotetradecane-8-ethanamine ( 10 ) show that, in both cases, the Cu²⁺ is pentacoordinated by the four donor atoms of the macrocycle and the amino group of the side chain. In aqueous solution, however, two forms of the complexes with stoichiometries [MLH] and [ML] (M = Cu²⁺ or Ni²⁺) have been observed. In [MLH], the amino group is protonated and does not bind to the metal ion, whereas in [ML] the amino group is bound, and a pentacoordinated geometry results. The pK_a values for the equilibrium [ML] + H⁺?[MLH]⁺ decrease in the order 12 > 10 > 3 , indicating that the 2-aminoethyl side chain binds better to the Cu²⁺ than the 3-aminopropyl side chain. Cyclic voltammetry for the Cu²⁺/Cu⁺ pair shows that the 2-aminoethyl pendant arm stabilizes the Cu²⁺ oxidation state, when the metal ion is in the 14-membered ring ( 10 ), whereas it stabilizes Cu⁺ for the 12-membered macrocycle ( 3 ).     

A Dual‐Response [2]Rotaxane Based on a 1,2,3‐Triazole Ring as a Novel Recognition Station

Two novel multilevel switchable [2]rotaxanes containing an ammonium and a triazole station have been constructed by a Cu^I‐catalyzed azide–alkyne cycloaddition reaction. The macrocycle of [2]rotaxane containing a C6‐chain bridge between the two hydrogen bonding stations exhibits high selectivity for the ammonium cation in the protonated form. Interestingly, the macrocycle is able to interact with the two recognition stations when the bridge between them is shortened. Upon deprotonation of both [2]rotaxanes, the macrocycle moves towards the triazole recognition site due to the hydrogen‐bond interaction between the triazole nitrogen atoms and the amide groups in the macrocycle. Upon addition of chloride anion, the conformation of [2]rotaxane is changed because of the cooperative recognition of the chloride anion by a favorable hydrogen‐bond donor from both the macrocycle isophthalamide and thread triazole CH proton.     

Synthesis and anion binding properties of 1,8-disulfonamidocarbazole dipyrromethane Schiff-base macrocycle & its amine analogue

A novel 1,8-disulfonamidocarbazole-dipyrromethane Schiff-base macrocycle (1) and its amine analogue (2) were designed and synthesised, and their anion binding properties were studied via UV–vis and ¹H NMR titration spectra. The obtained results showed that a small change in the macrocyclic structure (by reducing imines into the corresponding amines) produced a remarkable impact on its binding affinity and selectivity for anions. For example, macrocycle 1 displayed a 7.9:1 F^?/H₂PO₄^? selectivity; however, its amine analogue 2 showed a 78.5:1 F^?/H₂PO₄^? selectivity.