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Peter Comba

Publications and source records attributed to Peter Comba.

31 records · Page 2Linked to original sources
PubMed2002

Structural variation in transition-metal bispidine compounds.

The experimentally determined molecular structures of 40 transition metal complexes with the tetradentate bispyridine-substituted bispidone ligand, 2,4-bis(2-pyridine)-3,7-diazabicyclo[3.3.1]nonane-9-one [M(bisp)XYZ]n+; M = CrIII, MnII, FeII, CoII, CuII, CuI, ZnII; X, Y, Z = mono- or bidentate co-ligands; penta-, hexa- or heptacoordinate complexes) are characterized in detail, supported by force-field and DFT calculations. While the bispidine ligand is very rigid (N3...N7 distance = 2.933 +/- 0.025 A), it tolerates a large range of metal-donor bond lengths (2.07 A < sigma(M-N)/4 < 2.35 A). Of particular interest is the ratio of the bond lengths between the metal center and the two tertiary amine donors (0.84 A < M-N3/M-N7 < 1.05 A) and the fact that, in terms of this ratio there seem to be two clusters with M-N3 < M-N7 and M-N3 > or = M-N7. Calculations indicate that the two structural types are close to degenerate, and the structural form therefore depends on the metal ion, the number and type of co-ligands, as well as structural variations of the bispidine ligand backbone. Tuning of the structures is of importance since the structurally differing complexes have very different stabilities and reactivities.

Journal Article↗
PubMed2002

Copper-bispidine coordination chemistry: syntheses, structures, solution properties, and oxygenation reactivity.

Copper(I) and copper(II) complexes of two mononucleating and four dinucleating tetradentate ligands with a bispidine backbone (2,4-substituted (2-pyridyl or 4-methyl-2-pyridyl) 3,7-diazabicyclo[3.3.1]nonanone) have been prepared and analyzed structurally, spectroscopically, and electrochemically. The structures of the copper chromophores are square pyramidal, except for two copper(I) compounds which are four-coordinate with one noncoordinated pyridine. The other copper(I) structures have the two pyridine donors, the co-ligand (NCCH(3)), and one of the tertiary amines (N3) in-plane with the copper center and the other amine (N7) coordinated axially (Cu-N3 > Cu-N7, approximately 2.25 A vs 2.20 A). The copper(II) compounds with pyridine donors have a similar structure, but the axial amine has a weaker bond to the copper(II) center (Cu-N3 < Cu-N7, approximately 2.03 A vs 2.30 A). The structures with methylated pyridine donors are also square pyramidal with the co-ligands (Cl(-) or NCCH(3)) in-plane. With NCCH(3) the same structural type as for the other copper(II) complexes is observed, and with the bulkier Cl(-) the co-ligand is trans to N7, leading to a square pyramidal structure with the pyridine donors rotated out of the basal plane and only a small difference between axial and in-plane amines (2.15, 2.12 A). These structural differences, enforced by the rigid bispidine backbone, lead to large variations in spectroscopic and electrochemical properties and reactivities. Oxygenation of the copper(I) complexes with pyridine-substituted bispidine ligands leads to relatively stable mu-peroxo-dicopper(II) complexes; with a preorganization of the dicopper chromophores, by linking the two donor sets, these peroxo compounds are stable at room temperature for up to 1 h. The stabilization of the peroxo complexes is to a large extent attributed to the square pyramidal coordination geometry with the substrate bound in the basal plane, a structural motif enforced by the rigid bispidine backbone. The stabilities and structural properties are also seen to correlate with the spectroscopic (UV-vis and Raman) and electrochemical properties.

Chemical Phenomena↗
PubMed2002

Synthesis and structural properties of patellamide A derivatives and their copper(II) compounds.

The synthesis, characterization and copper(II) coordination chemistry of three new cyclic peptide ligands, PatJ(1) (cyclo-(Ile-Thr-(Gly)Thz-Ile-Thr-(Gly)Thz)), PatJ(2) (cyclo-(Ile-Thr-(Gly)Thz-(D)-Ile-Thr-(Gly)Thz)), and PatL (cyclo-(Ile-Ser-(Gly)Thz-Ile-Ser-(Gly)Thz)) are reported. All of these cyclic peptides and PatN (cyclo-(Ile-Ser-(Gly)Thz-Ile-Thr-(Gly)Thz)) are derivatives of patellamide A and have a [24]azacrown-8 macrocyclic structure. All four synthetic cyclic peptides have two thiazole rings but, in contrast to patellamide A, no oxazoline rings. The molecular structure of PatJ(1), determined by X-ray crystallography, has a saddle conformation with two close-to-coparallel thiazole rings, very similar to the geometry of patellamide D. The two coordination sites of PatJ(1) with thiazole-N and amide-N donors are each well preorganized for transition metal ion binding. The coordination of copper(II) was monitored by UV/Vis spectroscopy, and this reveals various (meta)stable mono- and dinuclear copper(II) complexes whose stoichiometry was confirmed by mass spectra. Two types of dinuclear copper(II) complexes, [Cu(2)(H(4)L)(OH(2))(n)](2+) (n=6, 8) and [Cu(2)(H(2)L)(OH(2))(n)] (n=4, 6; L=PatN, PatL, PatJ(1), PatJ(2)) have been identified and analyzed structurally by EPR spectroscopy and a combination of spectra simulations and molecular mechanics calculations (MM-EPR). The four structures are similar to each other and have a saddle conformation, that is, derived from the crystal structure of PatJ(1) by a twist of the two thiozole rings. The small but significant structural differences are characterized by the EPR simulations.

Amides↗
PubMed2002

A new molecular mechanics force field for the oxidized form of blue copper proteins.

A molecular mechanics force field for blue copper proteins has been developed, based on a rigid potential energy surface scan of the Cu(II)/His/His/Cys/Met chromophore, using DFT (B3LYP) calculations and the AMBER force field for the protein backbone. The strain-energy-minimized structures of the model chromophore alone are in excellent agreement with the DFT-optimized structure, and those of the entire set of cupredoxins (five structures are considered) are, within the experimental error limits, in good agreement with the single crystal structural data. However, the structural variation in the computed structures is much smaller than those in the experimental structures. It is shown that, due to the large error limits in the experimental data, a validation of the force field with experimental structural data is impossible because, within the error limits, all experimental structures considered are virtually identical. A validation on the basis of spectroscopic data and their correlation with experimental and computed structural data is proposed, and, as a first example, the correlation of intensity ratios of the charge transfer transitions with a specific distortion mode is presented. The quality of the correlation, using the computed structures, is higher than that with the X-ray structures, and this indicates that the computed structures are meaningful.

Azurin↗
PubMed1999

Bis-macrocyclic Ligands with Two Ferrocenyl End Groups, and Their Tetranuclear Dicopper(I) Compounds.

A series of bismacrocyclic ligands with two ferrocenyl groups, exo/endo-1,1':1' ',1' "-[1,2,4,5-tetrakis(5-aza-2-thiahexa-5-enyl)benzene]bisferrocene (exo/endo-FeBeFe), 1,1':1' ',1' "-[1,2:1',2'-tetrakis(5-aza-2-thiahexa-5-enyl)ethene]bisferrocene (1,2-FeEnFe), 1,1':1' ',1' "-[1,1':2,2'-tetrakis(5-aza-2-thiahexa-5-enyl)ethene]bisferrocene (1,1-FeEnFe), 1,1':1' ',1' "-[tetrakis(5-aza-2-thiahexa-5-enyl)methane]bisferrocene (FeMeFe), and their dicopper(I) compounds have been synthesized and characterized (electrochemistry, IR, NMR and Mössbauer spectroscopy). The molecular structure of endo-FeBeFe has been determined by X-ray structure analysis and the copper(I)-induced discrimination of the exo- and endo-isomers of FeBeFe has been investigated by (1)H NMR spectroscopy. The interaction between copper and iron in the tetranuclear compounds is discussed on the basis of the electrochemical and spectroscopic data.

Journal Article↗
PubMed1998

The Solution Structure of a Copper(II) Compound of a New Cyclic Octapeptide by EPR Spectroscopy and Force Field Calculations.

A new cyclic octapeptide, cyclo(Ile-Ser-(Gly)Thz-Ile-Thr-(Gly)Thz) (PatN), related to patellamide A, has been synthesized and reacted with copper(II) and base to form mono- and dinuclear complexes. The coordination environments around copper(II) have been characterized by EPR spectroscopy. The solution structure of the thermodynamically most stable product, a purple dicopper(II) compound, has been examined by simulating weakly dipole-dipole coupled EPR spectra based upon structural parameters obtained from force field (MM and MD) calculations. The MM-EPR method produces a saddle-shaped structure for [Cu(2)(PatN)(OH(2))(6)] that is similar to the known solution structure of patellamide A and the known solid-state structure of [Cu(2)(AscidH(2))CO(3)(OH(2))(2)]. Compared with the latter, [Cu(2)(PatN)] has no carbonate bridge and a significantly flatter topology. The MM-EPR approach to solution-structure determination for paramagnetic metallopeptides may find wide applications to other metallopeptides and metalloproteins.

Journal Article↗
PubMed1998

Helical Figure-of-Eight Loop Dicopper(I) Compounds: Syntheses, Structures, and Dynamics.

The synthesis of a series of nine large macrocyclic ligands with two N(2)S(2) (thioether and Schiff-base imine) binding sites each, with different bridges between the donor atoms of each site (ethylene, o-xylylene, propylene, butylene) and different spacer groups between the two binding sites (p-xylylene, 2,5-dimethyl-p-xylylene, 2,5-dimethoxy-p-xylylene), and the synthesis of a similar ligand with a preorganized double-helical geometry, based on a paracyclophane spacer group, are reported, together with the syntheses and characterizations of the corresponding dicopper(I) compounds. The solid state structures of the dicopper(I) complexes have two tetrahedral copper(I) sites, separated by ca. 8 Å, and a figure-of-eight loop configuration of the ligand with a parallel arrangement of the two substituted benzene spacer groups (benzene.benzene distance of ca. 3.5 Å). All the dicopper(I) compounds have the same double-helical configuration ("twisted ring figure-of-eight loop"). NMR spectroscopy indicates that the monocyclic metal-free ligands have an open, cyclic structure in solution, while the dicopper(I) compounds are folded as in the solid. In acetonitrile there is a fast dynamic equilibrium between two enantiomeric forms of the double-helical dicopper(I) compounds. The fact that copper(I)-donor atom bond breaking is involved in this process is supported by (1)H NMR data and by the X-ray crystal structure analysis of a putative intermediate with each of the two copper(I) centers coordinated to one acetonitrile and three donors of the macrocycle. A second fast dynamic, solvent independent process (epimerization) has been identified in nitromethane and acetonitrile, involving helix inversion with full conservation of the copper(I) coordination.

Journal Article↗
PubMed1998

Preparation, Structure, and Electronic Properties of a Low-Spin Iron(II) Hexaamine Compound.

[Fe(trans-diammac)](2+) (trans-diammac) = exo-6,13-diamino-6,13-dimethyl-1,4,8,11-tetraazatetradecane) is one of the very few fully characterized examples of a low-spin iron(II) compound with saturated amine ligands. The crystal structure analysis (monoclinic, P2(1)/c; a = 9.547(8), b = 14.631(13), c = 16.91(2) Å; beta = 98.92(7) degrees; Z = 4) defines the iron(II) coordination geometry as distorted octahedral with very short in-plane Fe-N distances (average of 2.01 Å) to the secondary amines of the macrocyclic ligand and slightly longer distances to the pendant primary amine donors (2.03 Å); there is a considerable tilt of the vector involving the axial donors with respect to the plane defined by the secondary amines and the metal center (theta = 11.5 degrees ). The metal-donor distances are shorter than those for other low-spin iron(II) hexaamines, and consequently, the redox potential (Fe(3+/2+)) is very small (0.45 V vs SHE) and the ligand field splitting is very large (Dq = 1785 cm(-)(1)). The structural, magnetic, and spectroscopic properties are discussed on the basis of the experimental data in comparison with model studies.

Journal Article↗
PubMed1998

Structural, EPR, and Electrochemical Studies of Binuclear Copper(II) Complexes of Bis(pentadentate) Ligands Derived from Bis(1,4,7-triazacyclonane) Macrocycles.

Structural, electrochemical, and EPR studies of binuclear copper(II) complexes of bis(pentadentate) ligands, obtained by attaching 2-pyridylmethyl arms to the four secondary nitrogens of bis(tacn) macrocycles linked by ethyl (tmpdtne, [Cu(2)(tmpdtne)](ClO(4))(4).2H(2)O 2), propyl (tmpdtnp, [Cu(2)(tmpdtnp)](ClO(4))(4) 3), butyl (tmpdtnb, [Cu(2)(tmpdtnb)](ClO(4))(4) 4), m-xylyl (tmpdtnm-X, [Cu(2)(tmpdtnm-X)](ClO(4))(4).2DMSO.2H(2)O, 5), and 2-propanol (tmpdtnp-OH, [Cu(2)(tmpdtnp-OH)](ClO(4))(4).2H(2)O, 6) bridges, are reported, together with further analysis of the mononuclear complex, [Cu(dmptacn)](ClO(4))(2) 1, dmptacn = 1,4-bis(2-pyridylmethyl)-1,4,7-triazacyclononane. Single-crystal X-ray diffraction studies established the molecular structure of 3 and the tetrakis(DMF) solvate of 4. Complex 3 crystallizes in the monoclinic space group P2(1)/c (No. 14) with a = 13.867(3), b = 13.548(6), c = 28.055(4) Å, beta = 102.63(1) degrees, V= 5143(2) Å(3), and Z = 4. Refinement gave R = 0.085 and R(w) = 0.089 for 3696 observed reflections. 4 crystallizes in the triclinic space group &Pmacr; (No. 2) with a = 11.775(4), b = 12.718(3), c = 13.201(3) Å, alpha = 61.25(2), beta = 75.99(3), gamma = 77.66(3) degrees, V = 1673(1) Å(3), and Z = 1. Refinement gave R = 0.072 and R(w) = 0.065 for 3876 observed reflections. In 4, the pentadentate compartments are oriented in an anti configuration, while in 3, constraints introduced by the propane bridging group result in a syn configuration. Both complexes exhibit distorted square pyramidal (SP) geometries about the Cu(II) centers with Cu-N(apical) approximately 2.25 Å and Cu-N(equatorial) approximately 2.0 Å. Molecular mechanics calculations have been carried out on these types of complexes for the first time in order to predict the solution structures of 5 and 6. The calculations revealed that the SP geometry is also preferred by these complexes and that there is little energy difference between the syn and anti configurations. Cyclic, square-wave, and steady-state voltammetric studies on 1-6 indicate that, on the time scale of the measurements, 1 undergoes a one-electron reduction to the Cu(I) state while 2-6 undergo an overall two-electron reduction to the binuclear Cu(I) complexes. For 2-4, a shift in reduction potential to more negative values with increasing Cu.Cu separation reflects the stabilization of the Cu(II) state while the two partially resolved reduction processes for 6 suggest that the alcohol group in the ligand backbone promotes a small level of interaction between copper centers.

Journal Article↗
PubMed1997

Novel Ring Contraction Reaction for the Synthesis of Functionalized Tetrathiamacrocyclic Ligand Molecules.

Chlorination of [14]aneS(4)-ol (1,4,8,11-tetrathiatetradecan-6-ol) and cis/trans-[14]aneS(4)-diol (cis/trans-1,4,8,11-tetrathiatetradecane-6,13-diol) yields the corresponding dichloro-substituted macrocycles [14]aneS(4)-Cl (1,4,8,11-tetrathiatetradecane 6-chloride) and cis/trans-[14]aneS(4)-Cl(2) (cis/trans-1,4,8,11-tetrathiatetradecane 6,13-dichloride) in good yield. Thiomethylation of the chlorides produces the ring-contracted pendent thioether macrocycles [13]aneS(4)-CH(2)SCH(3) (1,4,7,10-tetrathiatridecane-5-(methylthio)methane) and cis/trans-anti-[12]aneS(4)-(CH(2)SCH(3))(2) (1,4,7,10-tetrathiadodecane-5,11-bis((methylthio)methane)). The mechanism of the ring contraction reaction is discussed in terms of the reactivity of the monochlorinated macrocycle toward ring contraction and the stereochemistry of the chlorinated intermediates and the thiomethylated products, which are based on the X-ray crystal structure analyses of trans-[14]aneS(4)-Cl(2) and trans-anti-[12]aneS(4)-(CH(2)SCH(3))(2).

Journal Article↗
PubMed1997

Modeling of the Redox Properties of (Hexaamine)cobalt(III/II) Couples.

The thermodynamics (redox potentials) and kinetics (electron transfer rates) of (hexaamine)cobalt(III/II) redox couples are interpreted in terms of steric strain induced by the ligand systems. The intersections of potential energy curves (strain energy versus metal-ligand distance plots of pairs of conformers) of the oxidized and reduced forms of a wide range of (hexaamine)cobalt(III/II) couples are related to the inner sphere reorganization (DeltaH()), and correlated with experimentally determined electron self-exchange rates. The minima of these potential energy curves of the reduced and oxidized forms are correlated with the reduction potentials. The perturbation by electronic effects due to differences in nucleophilicity along the series ammonia, primary amine, secondary amine, tertiary amine has been accounted for. The redox potentials of the couples studied (E degrees = -0.6V to +0.8 V; vs SHE), the electron self-exchange rates (10(-)(7)s(-)(1)-10(3)s(-)(1)), the Co(3+)-N distances (1.94-2.05 Å), and the ligand field strengths (Co(3+): (1)A(1) -->( 1)T(1), 16 700-22 200 cm(-)(1)) cover a wide range. Accurate computed values for extremely long Co(3+)-N bonds and for the corresponding low ligand field parameters (MM-AOM), high redox potentials, and specific electron self-exchange rates could only be obtained with a modification of the originally used force field, involving Morse potentials for the metal-ligand bonds. Applications of these methods, involving the design of new oxidants or reductants with specific potentials and electron transfer rates, and the determination of solution structures based on experimentally determined redox properties are presented, limits of this purely steric approach are discussed, and alternatives are evaluated.

Journal Article↗
PubMed1997

Modeling of End-On (&mgr;-Peroxo)dicopper(II) Complexes.

A force field for (&mgr;-peroxo)dicopper(II) complexes was developed, based on a well-established parameter set for copper(II) complexes, the structural and spectroscopic data of a (&mgr;-peroxo)dicopper(II) complex with tris(2-pyridylmethylamine) donors and a series of (&mgr;-peroxo)dicobalt(III) compounds. This force field is shown to well reproduce the structural properties of the available structures of (&mgr;-peroxo)dicopper(II) and (&mgr;-peroxo)dicobalt(III) complexes, and it was used to compute a series of (&mgr;-peroxo)dicopper(II) compounds with two tris(2-pyridylmethylamin) units linked by different organic spacers at a 5-pyridyl position at each tetradentate moiety. The computed structures and strain energies indicate that (i) in the compound with an ethyl spacer group the ligand induces a considerable strain and distortion in the &mgr;-peroxo product, and these effects compensate the favorable entropy effects due to the ligand preorganization, in agreement with the published experimental results; (ii) the (&mgr;-peroxo)dicopper(II) compound with the propyl-linked ligand is relatively unstrained and structurally very similar to the parent compound; and (iii) larger spacer groups lead to rather distorted (&mgr;-peroxo)dicopper(II) products.

Journal Article↗