PubMed Health⌕ Search

Biomedical subjects

Christopher J Cramer

Publications and source records attributed to Christopher J Cramer.

At least 37 records · Page 2Linked to original sources
PubMed2006

Characterization of the structure and reactivity of monocopper-oxygen complexes supported by beta-diketiminate and anilido-imine ligands.

Copper-oxygen complexes supported by beta-diketiminate and anilido-imine ligands have recently been reported (Aboelella et al., J Am Chem Soc 2004, 126, 16896; Reynolds et al., Inorg Chem 2005, 44, 6989) as potential biomimetic models for dopamine beta-monooxygenase (DbetaM) and peptidylglycine alpha-hydroxylating monooxygenase (PHM). However, in contrast to the enzymatic systems, these complexes fail to exhibit C--H hydroxylation activity (Reynolds et al., Chem Commun 2005, 2014). Quantum chemical characterization of the 1:1 Cu-O(2) model adducts and related species (Cu(III)-hydroperoxide, Cu(III)-oxo, and Cu(III)-hydroxide) indicates that the 1:1 Cu-O(2) adducts are unreactive toward substrates because of the weakness of the O--H bond that would be formed upon hydrogen-atom abstraction. This in turn is ascribed to the 1:1 adducts having both low reduction potentials and basicities. Cu(III)-oxo species on the other hand, determined to be intermediate between Cu(III)-oxo and Cu(II)-oxyl in character, are shown to be far more reactive toward substrates. Based on these results, design strategies for new DbetaM and PHM biomimetic ligands are proposed: new ligands should be made less electron rich so as to favor end-on dioxygen coordination in the 1:1 Cu-O(2) adducts. Comparison of the relative reactivities of the various copper-oxygen complexes as hydroxylating agents provides support for a Cu(II)-superoxide species as the intermediate responsible for substrate hydroxylation in DbetaM and PHM, and suggests that a Cu(III)-oxo intermediate would be competent in this process as well.

Binding Sites↗
PubMed2005

Models for dioxygen activation by the CuB site of dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase.

On the basis of spectroscopic and crystallographic data for dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase (PHM), a variety of ligand sets have been used to model the oxygen-binding Cu site in these enzymes. Calculations which employed a combination of density functional and multireference second-order perturbation theory methods provided insights into the optimal ligand set for supporting eta (1) superoxo coordination as seen in a crystal structure of a precatalytic Cu/O(2) complex for PHM (Prigge et al. in Science 304:864-867, 2004). Anionic ligand sets stabilized eta (2) dioxygen coordination and were found to lead to more peroxo-like Cu-O(2) complexes with relatively exergonic binding free energies, suggesting that these adducts may be unreactive towards substrates. Neutral ligand sets (including a set of two imidazoles and a thioether), on the other hand, energetically favored eta (1) dioxygen coordination and exhibited limited dioxygen reduction. Binding free energies for the 1:1 adducts with Cu supported by the neutral ligand sets were also higher than with their anionic counterparts. Deviations between the geometry and energetics of the most analogous models and the PHM crystal structures suggest that the protein environment influences the coordination geometry at the Cu(B) site and increases the lability of water bound to the preoxygenated reduced form. Another implication is that a neutral ligand set will be critical in biomimetic models in order to stabilize eta (1) dioxygen coordination.

Binding Sites↗
PubMed2005

Quantum chemical characterization of the structures, thermochemical properties, and singlet-triplet splittings of didehydroquinolinium and didehydroisoquinolinium ions.

Structural and energetic properties are predicted for the 21 didehydroquinolinium ion isomers and 21 didehydroisoquinolinium ion isomers in their lowest-energy singlet and triplet states by using density functional and multireference second-order perturbation theories. Singlet-triplet splittings and biradical stabilization energies are examined to gain insight into the degree of interaction between the biradical centers, with comparison being made to analogous didehydronaphthalenes and didehydropyridines.

Free Radicals↗
PubMed2005

High-spin and low-spin iron(II) complexes with facially-coordinated borohydride ligands.

Rare examples of monometallic high-spin and low-spin L3Fe(H3BH) complexes have been characterized, where the two L3 ligands are [TpPh2] and [PhBP3] ([TpPh2] = [HB(3,5-Ph2pz)3]- and [PhBP3] = [PhB(CH2PPh2)3]-). The structures are reported wherein the borohydride ligand is facially coordinated to the iron center in each complex. Density functional methods have been employed to explain the bonding in these unusual iron(II) centers. Despite the differences in spin states, short Fe-B distances are observed in both complexes and there is significant theoretical evidence to support a substantial bonding interaction between the iron and boron nuclei. In light of this interaction, we suggest that these complexes can be described as (L3)Fe(eta4-H3BH) complexes.

Borohydrides↗
PubMed2005

How useful are vibrational frequencies of isotopomeric O2 fragments for assessing local symmetry? Some simple systems and the vexing case of a galactose oxidase model.

The tendency for mixed-isotope O2 fragments to exhibit different stretching frequencies in asymmetric environments is examined with various levels of electronic structure theory for simple peroxides and peroxyl radicals, as well as for a variety of monocopper-O2 complexes. The study of the monocopper species is motivated by their relevance to the active site of galactose oxidase. Extensive theoretical work with an experimental model characterized by Jazdzewski et al. (J. Biol. Inorg. Chem. 8:381-393, 2003) suggests that the failure to observe a splitting between 16O18O and 18O16O isotopomers cannot be taken as evidence against end-on O2 coordination. Conformational analysis on an energetic basis, however, is complicated by biradical character inherent in all of the copper-O2 singlet structures.

Algorithms↗
PubMed2005

Ab initio molecular orbital and density functional studies on the solvolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX-like compound.

[reaction: see text] Potential energy surfaces for the alkaline hydrolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX model compound, and the perhydrolysis of the latter have been computed at the MP2/6-31+G(d)//mPW1K/MIDI! level of theory. The effect of aqueous solvation was accounted for via the integral equation formalism polarizable continuum model (IEF-PCM) at the HF/6-31+G(d) level. Excellent agreement with the experimental enthalpy of activation for alkaline hydrolysis of sarin was found. For the alkaline hydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that the P-O and P-S bond cleavage processes are kinetically competitive but that the products of P-S bond cleavage are thermodynamically favored. For the perhydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that P-O bond cleavage is not kinetically competitive with P-S bond cleavage. In both cases, the data support initial formation of trigonal bipyramidal intermediates and demonstrate kinetic selectivity for nucleophilic attack on the face opposite the more apicophilic methoxide ligand.

Alkalies↗
PubMed2005

Characterization of a 1:1 Cu-O2 adduct supported by an anilido imine ligand.

Copper(I) complexes of sterically hindered anilido imine ligands o-C6H4{N(C6H3(i)Pr2)}{C(R)=NC6H3(i)Pr2}- (L(1), R = H; L(2), R = CH3) have been prepared and characterized by spectroscopic and X-ray crystallographic methods. These complexes are highly reactive with O2, and in the case of L2 the product of low-temperature oxygenation was fully characterized by spectroscopic, X-ray crystallographic, and computational methods. The resonance Raman spectrum features an isotope-sensitive vibration at 974 cm(-1) (Delta(18O) = 66 cm(-1)), consistent with assignment as an O-O stretch. Despite the asymmetric coordination environment provided by the supporting anilido imine ligand, the X-ray crystal structure confirms rather symmetric side-on binding of the O2 moiety to the copper center, and the O-O bond length of 1.392(2) Angstroms indicates that this intermediate has significant Cu(III)-peroxo character. Theoretical calculations support this interpretation and predict that while a fully optimized end-on singlet geometry can be obtained, it is higher in energy than the side-on isomer by 3.5 kcal mol(-1) at the CASPT2/TZP level.

Anilides↗
PubMed2005

Kinetics and DFT studies on the reaction of copper(II) complexes and H2O2.

Copper(II) complexes supported by bulky tridentate ligands L1(H) (N,N-bis(2-quinolylmethyl)-2-phenylethylamine) and L1(Ph) (N,N-bis(2-quinolylmethyl)-2,2-diphenylethylamine) have been prepared and their crystal structures as well as some physicochemical properties have been explored. Each complex exhibits a square pyramidal structure containing a coordinated solvent molecule at an equatorial position and a weakly coordinated counter anion (or water) at an axial position. The copper(II) complexes reacted readily with H(2)O(2) at a low temperature to give mononuclear hydroperoxo copper(II) complexes. Kinetics and DFT studies have suggested that, in the initial stage of the reaction, deprotonated hydrogen peroxide attacks the cupric ion, presumably at the axial position, to give a hydroperoxo copper(II) complex retaining the coordinated solvent molecule (H(R).S). H(R).S then loses the solvent to give a tetragonal copper(II)-hydroperoxo complex (H(R)), in which the -OOH group may occupy an equatorial position. The copper(II)-hydroperoxo complex H(R) exhibits a relatively high O-O bond stretching vibration at 900 cm(-1) compared to other previously reported examples.

Copper↗
PubMed2005

Experimental and theoretical study of stabilization of delocalized forms of semibullvalenes and barbaralanes by dipolar and polarizable solvents. Observation of a delocalized structure that is lower in free energy than the localized form.

[reaction: see text] UV/vis spectra of thermochromic semibullvalenes 1 and barbaralanes 2, which undergo rapid degenerate Cope rearrangements, display temperature-dependent shoulders (1b, 1d, 1e) or absorption maxima (1c, 2c, 2f) at the low-energy side of their strong UV bands. These long-wavelength absorptions are ascribed to Franck-Condon transitions from delocalized structures 1(deloc) and 2(deloc). Gibbs free energy differences, DeltaG*, between delocalized and localized forms were calculated from the temperature dependence of the long-wavelength absorptions. Dipolar and polarizable solvents strongly affect and even may reverse the relative stabilities of the localized and delocalized forms of 1c, 2c, and 2f. For example, DeltaG*(2c) = 8 kJ mol(-)(1) in cyclohexane, 2 kJ mol(-)(1) in dimethylformamide, and -3 kJ mol(-)(1) in N,N'-dimethylpropylene urea (DMPU), so that (2c(deloc))(DMPU) becomes the global minimum. In contrast to the case for 2c, the intensities of the long-wavelength shoulders of the yellow semibullvalenes 1b, 1d, and 1e are only moderately influenced by solvents, and the rates of Cope rearrangements of the nonthermochromic, colorless barbaralanes 2a and 2b, determined by NMR methods, are almost solvent-invariant. In search of the solute properties that are decisive in determining the influence of solvent upon DeltaG*, electrical dipole and quadrupole moments and molecular polarizabilities have been calculated using the B3LYP/6-31G* method and solvation energies have been computed with the conductorlike polarized continuum model (CPCM). The results of these calculations indicate that the solvent effects are due to the greater polarity and polarizability of the delocalized structures relative to the localized structures.

Journal Article↗
PubMed2005

Demonstration of tunable reactivity for meta-benzynes.

A combined computational and experimental study on the gas-phase structures and reactivities of charged 1,3-didehydroarenes (meta-benzynes) demonstrates that the reactivity of such biradicals can be "tuned" by using appropriate substituents. Substituents that destabilize a specific zwitterionic resonance structure can change the reactivity of the biradical from mildly carbocationic to radical-like. These substituent effects are not the result of changes in the singlet-triplet gaps of the biradicals, but rather reflect changes in the potential energy surfaces for the dehydrocarbon separation.

Benzene Derivatives↗
PubMed2005

Oligomeric rods of alkyl- and hydridogallium imides.

Reaction of [RGa(NMe(2))(2)](2), where R = Me, Et, Bu, and Hx, with ammonia at 150 degrees C in an autoclave produced insoluble white powders formulated as oligomers of [RGaNH](n). The analogous reaction between NH(3) and MeGa[N(SiMe(3))(2)](2) at low temperature (<25 degrees C) formed an isolable intermediate, [MeGa(mu-NH(2))N(SiMe(3))(2)](2), that was characterized using single-crystal X-ray diffraction. Infrared spectroscopy and X-ray diffraction of the oligomers were consistent with a rodlike structure comprised of six-membered, [RGaNH](3) rings stacked perpendicular to the long axis of the rod. The method of synthesis, formula, and diffraction results suggested a structural similarity between the alkyl, [RGaNH](n)(), and the previously reported hydride, [HGaNH](n). The structural and electronic properties of rods having the general formula H(3)[(HXYH)(3)](n)H(3) (XY = GaN, GeC; n = 1-9) were investigated using density functional theory. Atomic electronegativity differences between the group 13/15 and 14/14 systems were found to play important roles in the geometrical structures of the two rods and also caused significant differences in the electronic structures. Energetically, it was found to be increasingly favorable to add additional cyclotrigallazane rings to the GaN rods, while for the GeC rods, there was a roughly constant energy cost associated with each additional ring. The electric dipole moments of the GaN rods increased substantially with length; in the GeC rods, charge separation occurred to a much smaller extent and had a polarization opposite to that found in GaN. In addition, increased dipole moments correlated with smaller electronic excitation energies, as predicted by time-dependent density functional theory. All of the powders exhibited luminescence in the visible spectrum at room temperature. Structure observed in the photoluminescence spectra of [HGaNH](n) and [MeGaNH](n) was interpreted as arising from rods of different length.

Journal Article↗
PubMed2004

Dioxygen activation at a single copper site: structure, bonding, and mechanism of formation of 1:1 Cu-O2 adducts.

To evaluate the fundamental process of O(2) activation at a single copper site that occurs in biological and catalytic systems, a detailed study of O(2) binding to Cu(I) complexes of beta-diketiminate ligands L (L(1) = backbone Me; L(2) = backbone tBu) by X-ray crystallography, X-ray absorption spectroscopy (XAS), cryogenic stopped-flow kinetics, and theoretical calculations was performed. Using synchrotron radiation, an X-ray diffraction data set for L(2)CuO(2) was acquired, which led to structural parameters in close agreement to theoretical predictions. Significant Cu(III)-peroxo character for the complex was corroborated by XAS. On the basis of stopped-flow kinetics data and theoretical calculations for the oxygenation of L(1)Cu(RCN) (R = alkyl, aryl) in THF and THF/RCN mixtures between 193 and 233 K, a dual pathway mechanism is proposed involving (a) rate-determining solvolysis of RCN by THF followed by rapid oxygenation of L(1)Cu(THF) and (b) direct, bimolecular oxygenation of L(1)Cu(RCN) via an associative process.

Binding Sites↗
PubMed2004

Modeling the peroxide/superoxide continuum in 1:1 side-on adducts of O2 with Cu.

The character of singlet (C(3)N(2)H(5))CuO(2) ranges smoothly between copper(III) peroxide and copper(II) superoxide with variation of the electronic character of the supporting beta-diketiminate ligand. Over the range of the variation, multireference second-order perturbation theory predicts the (1)A(1) singlet state always to be lower in energy than the lowest triplet state ((3)B(1)). The multideterminantal character of the biradical-like superoxide mesomer causes density functional theory sometimes to fail badly in predicting the relative energies of these same states, although its predictions of other properties, such as geometry, are of good quality.

Journal Article↗
PubMed2004

Interactions of alkyltin salts with biological dithiols: dealkylation and induction of a regular beta-turn structure in peptides.

Organotin compounds specifically target vicinal dithiols, thereby inhibiting the function of essential enzymes. Here, we present the NMR binding studies of trimethyltin (TMT) and dimethyltin (DMT) chlorides with a linear peptide (ILGCWCYLR) derived from the membrane protein stannin (SNN). We show that this peptide is able to dealkylate TMT and bind DMT, adopting a stable type-I beta-turn conformation. Both the NMR data and the calculated structures indicate that the two cysteines coordinate the tin atom in a distorted tetrahedral geometry. The molecular geometries and tin coordination state were confirmed using density functional theory (DFT). In addition, NMR spectral parameters back calculated from the DFT minimized structure compared well with experimental data. These results in conjunction with studies on peptide variants (i.e., C4S, C6S, and Y7F) demonstrate unequivocally the key role of biological dithiols in both the dealkylation and binding of organotin compounds. This peptide serves as a model system for alkyltin-protein interactions and gives new insights into the biological fate of alkyltin compounds.

Alkylation↗
PubMed2004

Effect of meta electron-donating groups on the electronic structure of substituted phenyl nitrenium ions.

Density functional theory (UB3LYP/6-31G(d,p)) was used to determine substituent effects on the singlet-triplet-state energy gap for 21 meta-substituted phenylnitrenium ions. It was found that strongly electron-donating substituents stabilize the triplet state relative to the singlet state. With sufficiently strong meta electron donors (e.g., m,m'-diaminophenylnitrenium ion) the triplet is predicted to be the ground state. Analysis of equilibrium geometries, Kohn-Sham orbital distributions, and Mulliken spin densities for the triplet states of this series of nitrenium ions leads to the conclusion that there are two spatially distinct types of low-energy triplet states. Simple arylnitrenium ions such as phenylnitrenium ions as well as those having electron-withdrawing or weakly donating meta substituents have lowest-energy triplet states that are n,pi in nature. That is, one singly occupied molecular orbital is orthogonal to the plane of the phenyl ring and one is coplanar. These n,pi triplets are generally characterized by large ArNH bond angles (ca. 130-132 degrees ) and an NH bond that is perpendicular to the plane of the phenyl ring. In contrast, meta donor arylnitrenium ions have a lowest-energy triplet state best described as pi,pi. That is, both singly occupied molecular orbitals are orthogonal to the aromatic ring. Such pi,pi states are characterized by NH bonds that are coplanar with the phenyl ring and have ArNH bond angles that are more acute (ca. 110-111 degrees ). These triplet nitrenium ions have electronic structures analogous to those of meta-benzoquinodimethane derivatives.

Journal Article↗
PubMed2003

Effect of G-1 on histidine tRNA microhelix conformation.

Histidine tRNAs (tRNA(His)) are unique in that they possess an extra 5'-base (G-1) not found in other tRNAs. Deletion of G-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. To better understand the role of the G-1 nucleotide in defining the structure of tRNA(His), and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a DeltaG-1 mutant Escherichia coli histidine tRNA acceptor stem microhelix. Using NMR-derived distance restraints, global structural characteristics are described and interpreted to rationalize experimental observations with respect to aminoacylation activity. The quality of the NMR-derived solution conformations of the wild-type and DeltaG-1 histidine microhelices (micro helix(His)) is assessed using a variety of MD-based computational protocols. Most of the duplex regions of the acceptor stem and the UUCG tetraloop are well defined and effectively superimposable for the wild-type and DeltaG-1 mutant microhelix(His). Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3' tail. The wild-type microhelix(His) structure is more well defined than the mutant and folds into a 'stacked fold-back' conformation. In contrast, we observe fraying of the first two base pairs and looping back of the single-stranded region in the DeltaG-1 mutant resulting in a much less well defined conformation. Thus the role of the extra G-1 base of the unique G-1:C73 base pair in tRNA(His) may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3' region.

Base Sequence↗