Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

Labeling of the Neuropeptide Enkephalin with Functionalized Tris(pyrazolyl)borate Complexes: Solid-Phase Synthesis and Characterization of p-[Enk-OH]COC6H4TpPtMe3 and p-[Enk-OH]COC6H4TpMeRe(CO)3

Bioconjugates of the neuropeptide Enkephalin (Enk = -Tyr-Gly-Gly-Phe-Leu-) labeled with organotransition metal tris-pyrazolylborate (Tp) complexes are reported. p-[Enk-OH]COC6H4TpPtMe3 and p-[Enk-OH]COC6H4Tp(Me)Re(CO)3 have been synthesized by solid-phase peptide synthesis (SPPS), purified by RP-HPLC, and characterized by ESI-mass spectrometry and 1H NMR and IR spectroscopies. p-[Enk-OH]COC6H4TpPtMe3 and p-[Enk-OH]COC6H4Tp(Me)Re(CO)3 constitute the first examples of Tp complexes employed in SPPS.

Electrochemical recognition of anions by 1,1′-N,N′-ferrocenoylbisamino acid esters

A series of novel ferrocene-based receptors, 1,1'-N,N'-ferrocenoylbisamino acid methyl esters 2-5 have been prepared and their electrochemical properties determined. The amino acids employed were glycine (2), beta-alanine (3), gamma-aminobutyric acid (4) and l-norleucine (5). These receptors are composed of an electroactive core and two parallel strands of amino acids that can interact with anions via electrostatic interactions in the oxidized state as well as secondary interactions, such as hydrogen bonding and hydrophobic interactions. Furthermore, the semi-rigid molecular clefts between the two strands of amino acids in these receptors are capable of discerning anions of different geometries and sizes. The anion sensing capabilities of receptors 2-5 were studied using cyclic voltammetry (CV). The anions studied were chloride (Cl-), nitrate (NO3-), dihydrogen phosphate (H(2)PO(4)-), hydrogen sulfate (HSO(4)-), acetate (CH(3)COO-) and neurologically important anions such as lactate (CH(3)CH(OH)COO-), pyruvate (CH(3)COCOO-) and glutamate (HOOC-CH(NH2)CH(2)CH(2)COO-). The receptors 2-5 exhibit selectivity towards chloride, dihydrogen phosphate and acetate, over hydrogen sulfate and nitrate ions and generate a redox response in organic media. Also, binding studies of receptor 3 with neurologically important anions show it displays selectivity towards lactate and pyruvate, over glutamate ions and generates a redox response. However the response is ill defined in all cases, with poorly separated "free" and "ion-pair" peaks, which preclude accurate measurement of the response by CV. These results emphasize the considerations required for the design of ferrocene-based receptors and the necessary parameters for efficient electrochemical recognition of small anions by CV.

Solid-Phase Synthesis, Characterization, and Antibacterial Activities of Metallocene–Peptide Bioconjugates

This work shows how the introduction of an organometallic group enhances and modifies the specificity of biologically active peptides. Ferrocene was chosen as an organometallic group because it has been shown to alter the pharmacodynamic profile of bioactive compounds. A comparison with the isosteric cobaltocenium group allows one to explore the influence of charge and redox potential on the biological activity of the conjugates. Arginine and tryptophan containing peptides H-WRWRWR-NH(2) and H-RWRWRW-NH(2) and the metallocene peptide bioconjugates [M]-C(O)-RWRWR-NH(2) and [M]-C(O)-WRWRW-NH(2), where [M]=[Co(Cp)(C(5)H(4))](+), [Fe(Cp)(C(5)H(4))] were prepared by solid-phase peptide synthesis (SPPS). They were purified by HPLC, characterized by ESIMS and NMR spectroscopy, and tested for antibacterial properties against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus using the minimum inhibitory concentration (MIC) test. In most cases, no metal-specific activity could be observed. However, the conjugate [Fe(Cp)(C(5)H(4))-C(O)-WRWRW-NH(2)] 6 was found to be particularly effective against the Gram-positive S. aureus. The activity of this metallocene-pentapeptide conjugate (7.1 microM) was even better than the 20 amino acid naturally occurring pilosulin 2, which was used as a positive control. Unlike all other compounds tested, which were most active against the Gram-negative E. coli strain, the ferrocene conjugate 6 was the only compound in this series that was most active against Gram-positive bacteria. Given the health concerns resulting from multidrug resistant S. aureus strains, the incorporation of metallocenes may provide a novel line of attack.

Helically Chiral Ferrocene Peptides Containing 1′-Aminoferrocene-1-Carboxylic Acid Subunits as Turn Inducers

We present a detailed structural study of peptide derivatives of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca), one of the simplest organometallic amino acids. Fca was incorporated into di- to pentapeptides with D- and L-alanine residues attached to either the carboxy or amino group, or to both. Crystallographic and spectroscopic studies (circular dicroism (CD), IR, and NMR) of about two dozen compounds were used to gain a detailed insight into their structures in the solid state as well as in solution. Four derivatives were characterized by single-crystal X-ray analysis, namely Boc-Fca-Ala-OMe (16), Boc-Fca-D-Ala-OMe (17), Boc-Fca-beta-Ala-OMe (18), and Boc-Ala-Fca-Ala-Ala-OMe (21) (Boc=tert-butyloxycarbamyl). CD spectroscopy is an extremely useful tool to elucidate the helical chirality of the metallocene core. Unlike in all other known ferrocene peptides, the helical chirality of the ferrocene is governed solely by the chirality of the amino acid attached to the N terminus of Fca. Depending on the degree of substitution of both cyclopentadiene (Cp) rings, different hydrogen-bonding patterns are realized. (1)H NMR and IR spectroscopy, together with the results from X-ray crystallography, give detailed information regarding not only the hydrogen-bonding patterns of the compounds, but also the equilibria between different conformers in solution. Differences in chemical shifts of NH protons in dimethyl sulfoxide ([D(6)]DMSO) and CDCl(3), that is, the variation ratio (vr), is used for the first time as a measure of the hydrogen-bonding strength of individual COHN bonds in ferrocenoyl peptides. In dipeptides with one intramolecular hydrogen bond between the pendant chains, for example, in dipeptide 16, an equilibrium between hydrogen-bonded and open forms is observed, as testified by a vr value of around 0.5. Higher peptides, such as tetrapeptide 21, are able to form two intramolecular hydrogen bonds stabilizing one single conformation in CDCl(3) solution (vr approximately 0). Due to the low barrier of Cp-ring rotation, new and unnatural hydrogen-bonding patterns are emerging. The systematic work described herein lays a solid foundation for the rational design of metallocene peptides with unusual structures and properties.

Systematizing structural motifs and nomenclature in 1,n′-disubstituted ferrocene peptides

Ferrocene peptide conjugates display an array of structural features including helical ferrocene based chirality and a number of different intramolecular hydrogen bonding patterns. In this tutorial review we present a rigorous nomenclature for these systems, followed by a section that summarises and categorises the structures known to date. The issues discussed herein are of general relevance for all metallocene-based chiral transition metal catalysts and peptide turn mimetics.

Induction of γ-Turn-Like Structure in Ferrocene Bearing Dipeptide Chains via Conformational Control

[structure: see text] A combination of the ferrocene scaffold as a central reverse-turn unit with the dipeptide chains (-L-Pro-L-Ala-NHPy) was demonstrated to induce both inverse gamma-turn-like and antiparallel beta-sheet-like structures. Only the antiparallel beta-sheet-like structure was formed in the ferrocene bearing the heterochiral dipeptide chains (-L-Pro-D-Ala-NHPy), in which highly organized self-assembly was achieved through a network of intermolecular hydrogen bonds.

Amino acid conjugates of 1,1′-diaminoferrocene. Synthesis and chiral organization

1,1'-bis(tert-butoxycarbonylamino)ferrocene (6), a protected derivative of 1,1'-diaminoferrocene, has been synthesized by a very convenient method and serves as a synthon for 1,1'-diaminoferrocene. Its structure in solid state and in solution has been studied by NMR and X-ray crystallography. 1,1'-bis(tert-butoxycarbonylamino)ferrocene serves as starting material for the synthesis of amino acid conjugates of L- and D-alanine. The structures of these bioconjugates have been studied by NMR and CD spectroscopy and X-ray crystallography and reveal that the chiral organization of the podant amino acid chains is controlled by the chirality of the attached amino acid. The substituents engage in strong intramolecular H-bonding generating 14-membered H-bonded rings, a motif previously unrealized in ferrocene-amino acid and peptide conjugates.

Synthesis, structure and electrochemistry of ferrocene–peptide macrocycles

Redox active cyclopeptides Fc[CSA]2 (5), Fc[Gly-CSA]2 (6), Fc[Ala-CSA]2 (7), Fc[Val-CSA](2) and Fc[Leu-CSA]2 (9) (CSA = cysteamine) which are formed by the reaction of ferrocenedicarboxylic acid with peptide cystamines at high dilutions. These systems exhibit H-bonding involving the amide NH in solution as shown by their temperature dependent NMR spectra. With the exception of 5, the ferrocene macrocycles display intramolecular N...O cross-ring H-bonding in the solid state involving the amino acids proximal to the ferrocene.

The first oligopeptide derivative of 1′-aminoferrocene-1-carboxylic acid shows helical chirality with antiparallel strands

The unnatural organometallic amino acid 1'-aminoferrocene-1-carboxylic acid (Fca) induces a turn structure in a tetrapeptide with anti-parallel strands which is stabilized by two intra-molecular hydrogen bonds in the solid state and in solution.