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Biomedical subjects

Philip Coppens

Publications and source records attributed to Philip Coppens.

At least 19 recordsLinked to original sources
PubMed2006

On the design of ultrafast shutters for time-resolved synchrotron experiments.

A comprehensive treatment of the limitations and possibilities for single-pulse selection in synchrotron operating modes with approximately 150 ns bunch separation, as occurs in the standard operating mode at the Advanced Photon Source, is presented. It is shown that the strength of available materials and allowable kinetic energy build-up limit single-bunch selection for this separation to sample sizes of approximately 100 microm, and that for minimization of kinetic energy build-up it is preferable to increase the r.p.m. within physically acceptable limits rather than increase the disc radius to obtain a desirable peripheral speed. A slight modification of the equal-bunch spacing standard fill patterns is proposed that allows use of samples as large as 500 microm. The corresponding peripheral speed of the chopper wheel is approximately 600 m s(-1), which is within the limits of high-strength titanium alloys. For smaller samples, peripheral speeds are proportionally lower. Versatility can be achieved with interchangeable chopper wheels and the use of different orientations of the rotation axis relative to the X-ray beam, which opens the possibility of larger, rather than one-of-a-kind, production runs.

Equipment Design↗
PubMed2006

Effect of the environment on molecular properties: synthesis, structure, and photoluminescence of Cu(I) bis(2,9-dimethyl-1,10-phenanthroline) nanoclusters in eight different supramolecular frameworks.

By selection of different charge-balancing anionic frameworks and different host-to-guest ratios, the photosensitizer-dye cation [Cu(dmp)2]+ (dmp = 2,9-dimethyl-1,10-phenanthroline) has been embedded in a series of three-dimensional host structures. It occurs with variable geometry in different states of aggregation, including weakly interacting monomers, isolated dimers, columns, and layers. A large variation in its emission lifetime is correlated with the relative energy level spacings of the guest- and host-framework components. In a fully saturated host framework, the lifetime exceeds values reported for a series of conventional Cu(dmp)2 salts.

Journal Article↗
PubMed2006

On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model.

Accurate, yet simple and efficient, formulae are presented for calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) from the aspherical Hansen-Coppens pseudoatom model of electron density [Hansen & Coppens (1978). Acta Cryst. A34, 909-921]. They are based on the expansion of |r' - r|(-1) in spherical harmonics and the incomplete gamma function for a Slater-type function of the form R(l)(r) = r(n) exp(-alpha ). The formulae are valid for 0 < or = r < or = infinity and are easily extended to higher values of l. Special treatment of integrals is needed only for functions with n = l and n = l + 1 at r = 0. The method is tested using theoretical pseudoatom parameters of the formamide molecule obtained via reciprocal-space fitting of PBE/6-31G** densities and experimental X-ray data of Fe(CO)(5). The ESP, EF and EFG values at the nuclear positions in formamide are in very good agreement with those directly evaluated from density-functional PBE calculations with 6-31G**, aug-cc-pVDZ and aug-cc-pVTZ basis sets. The small observed discrepancies are attributed to the different behavior of Gaussian- and Slater-type functions near the nuclei and to imperfections of the reciprocal-space fit. An EF map is displayed which allows useful visualization of the lattice EF effects in the crystal structure of formamide. Analysis of experimental 100 K X-ray data of Fe(CO)(5) yields the value of the nuclear quadrupole moment Q((57)Fe(m)) = 0.12 x 10(-28) m(2) after taking into account Sternheimer shielding/antishielding effects of the core. This value is in excellent agreement with that reported by Su & Coppens [Acta Cryst. (1996), A52, 748-756] but slightly smaller than the generally accepted value of 0.16 +/- 5% x 10(-28) m(2) obtained from combined theoretical/spectroscopic studies [Dufek, Blaha & Schwarz (1995). Phys. Rev. Lett. 25, 3545-3548].

Journal Article↗
PubMed2006

Trinuclear gold(I) triazolates: a new class of wide-band phosphors and sensors.

A new cyclic gold(I) triazolate trimer, [Au(3,5-i-Pr2Tz)]3 (1), exhibits fully overlapping aurophilically bonded dimer-of-trimer units that lead to multiple phosphorescence bands in both the solid state and solution. The conformation of the hexanuclear unit exhibits reversible interconversion between C2 and D3 effective symmetries, depending on the crystal temperature or solution concentration, the variation of which leads to isoemissive and isosbestic points. Solutions of 1 exhibit remarkable quenching properties that demonstrate molecular recognition with high selectivity and hypersensitivity for some reagents, as influenced by protonation via Brønsted acids, pi intercalation, and/or energy transfer. The quenched phosphorescence of 1 by acetic acids can be regenerated by NEt3.

Journal Article↗
PubMed2006

Ligand-unsupported Au(I) chains with short Au(I)...Au(I) contacts.

A new series of solids with ligand-unsupported Au(I) chains with short Au...Au contacts were synthesized; as Ag compounds with the same structure are known, the new phases now allow unbiased comparison of Ag...Ag and Au...Au metallophilic bonds not supported by bridging ligands, which shows the latter to be consistently shorter by 0.03-0.04 A.

Journal Article↗
PubMed2006

Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials.

Intermolecular interaction energies between fragments of glycopeptide antibiotics and small peptide ligands are evaluated using geometries determined by X-ray crystallography and recently developed methods suitable for application to very large molecular complexes. The calculation of the electrostatic contributions is based on charge densities constructed with a databank of transferable aspherical atoms described by nucleus-centered spherical harmonic density functions, and uses the accurate and fast EPMM method. Dispersion, induction and exchange-repulsion contributions are evaluated with atom-atom potentials fitted to intermolecular energies from SAPT (symmetry-adapted perturbation theory) calculations on a large number of molecules. For a number of the complexes, first-principle calculations using density functional theory have been performed for comparison. Results of the new methods agree within reasonable bounds with those from DFT calculations, while being obtained at a fraction (less than 1%) of the computer time. A strong dependence on the geometry of the interaction is found, even when the number of hydrogen bonds between the substrate and antibiotic fragment is the same. While high-resolution X-ray data are required to obtain interaction energies at a quantitative level, the techniques developed have potential for joint X-ray/energy refinement of macromolecular structures.

Anti-Bacterial Agents↗
PubMed2006

Finding optimal radial-function parameters for S atoms in the Hansen-Coppens multipole model through refinement of theoretical densities.

The multipolar model of the valence-electron-density distribution for S atoms has been optimized based on theoretical structure factors for six organic molecules. The evaluation of different sets of radial function parameters shows that: (a) the ratio of the n(l) values for different l is more important than their absolute values, as parallel changes in all n(l) for a given atom are compensated for by a change in the refined value of the kappa' parameter, and (b) the (2,4,6,8) set of n(l) with kappa' refined as a single value is an optimal choice of radial function parameters for S atoms.

Journal Article↗
PubMed2006

Experimental and density functional theoretical investigations of linkage isomerism in six-coordinate FeNO(6) iron porphyrins with axial nitrosyl and nitro ligands.

A critical component of the biological activity of NO and nitrite involves their coordination to the iron center in heme proteins. Irradiation (330 < lambda < 500 nm) of the nitrosyl-nitro compound (TPP)Fe(NO)(NO(2)) (TPP = tetraphenylporphyrinato dianion) at 11 K results in changes in the IR spectrum associated with both nitro-to-nitrito and nitrosyl-to-isonitrosyl linkage isomerism. Only the nitro-to-nitrito linkage isomer is obtained at 200 K, indicating that the isonitrosyl linkage isomer is less stable than the nitrito linkage isomer. DFT calculations reveal two ground-state conformations of (porphine)Fe(NO)(NO(2)) that differ in the relative axial ligand orientations (i.e., GS parallel and GS perpendicular). In both conformations, the FeNO group is bent (156.4 degrees for GS parallel, 159.8 degrees for GS perpendicular) for this formally {FeNO}(6) compound. Three conformations of the nitrosyl-nitrito isomer (porphine)Fe(NO)(ONO) (MSa parallel, MSa perpendicular, and MSa(L)) and two conformations of the isonitrosyl-nitro isomer (porphine)Fe(ON)(NO(2)) (MSb parallel and MSb perpendicular) are identified, as are three conformations of the double-linkage isomer (porphine)Fe(ON)(ONO) (MSc parallel, MSc perpendicular, MSc(L)). Only 2 of the 10 optimized geometries contain near-linear FeNO (MSa(L)) and FeON (MSc(L)) bonds. The energies of the ground-state and isomeric structures increase in the order GS < MSa < MSb < MSc. Vibrational frequencies for all of the linkage isomers have been calculated, and the theoretical gas-phase absorption spectrum of (porphine)Fe(NO)(NO(2)) has been analyzed to obtain information on the electronic transitions responsible for the linkage isomerization. Comparison of the experimental and theoretical IR spectra does not provide evidence for the existence of a double linkage isomer of (TPP)Fe(NO)(NO(2)).

Crystallography, X-Ray↗
PubMed2005

Photoinduced oxygen transfer and double-linkage isomerism in a cis-(NO)(NO2) transition-metal complex by photocrystallography, FT-IR spectroscopy and DFT calculations.

Photocrystallographic experiments show that laser exposure of crystals of [Ru(bpy)2(NO)(NO2)](PF6)2 at 90 K produces a double isonitrosyl-nitrito linkage isomer and provide the detailed geometry of the metastable species generated. The analysis indicates that the isomerization is accomplished through an intramolecular redox reaction involving oxygen transfer from the nitro to the nitrosyl group. At 200 K only a single (nitrito) linkage isomer is formed with a U-shaped conformation of the nitrito group rather than the Z conformation observed at 90 K. A mechanism for the isomerization is proposed based on the crystallographic results and FTIR data collected at low temperatures during the isomerization process. The study presents the first structural evidence for double linkage isomerization in transition-metal complexes.

Journal Article↗
PubMed2005

A fast mechanical shutter for submicrosecond time-resolved synchrotron experiments.

A new high-speed high-repetition-rate X-ray beam shutter for time-resolved photocrystallography at synchrotron sources has been developed and tested. The new design is based on a commercially existing DC servomotor and a frequency-lock control capable linear amplifier. Accurate speed control combined with an air bearing results in extremely low jitter in the motor rotation. Measured jitter at rotation speeds of 12000 to 30000 r min-1 is less than 2 ns at a 6sigma confidence level. The chopper disc is interchangeable, allowing maximum flexibility. The chopper disc currently installed has 45 radial slots which allows synchronization from the 12th to the 20th subfrequencies of the orbit frequency of the Advanced Photon Source storage ring, corresponding to X-ray pulse frequencies of 13.6 to 22.6 kHz. At 30000 r min-1 the opening time window with a 350 microm slot size is 2.11 micros, and correspondingly less with smaller openings, which may be compared with the 3.68 micros orbit time of the Advanced Photon Source. The shutter provides high accuracy and efficient use of X-rays at a modest cost.

Journal Article↗
PubMed2005

On the refinement of time-resolved diffraction data: comparison of the random-distribution and cluster-formation models and analysis of the light-induced increase in the atomic displacement parameters.

Expressions for the random-distribution and cluster-formation models for light-induced changes in crystals studied by time-resolved diffraction are presented. The two models can be distinguished on the basis of differences in the predicted intensities. The light-induced increase in the atomic displacement parameters is analyzed with both simulated and experimental data sets.

Algorithms↗
PubMed2005

Two novel bis(2,9-dimethyl-1,10-phenanthroline)copper(I) complexes: [Cu(dmp)2]2(PF6)2.0.5(bpmh).CH3CN and [Cu(dmp)2][N(CN)2].

Two new salts of the cation [CuI(dmp)2]+ (dmp is 2,9-dimethyl-1,10-phenanthroline, C14H12N2), namely bis[bis(2,9-dimethyl-1,10-phenanthroline-kappa2N,N')copper(I)] bis(hexafluorophosphate) hemi[bis(4-pyridylmethylidene)hydrazine] acetonitrile solvate, [Cu(C14H12N2)2]2(PF6)2.0.5C12H10N4.C2H3N or [Cu(dmp)2]2(PF6)2.0.5(bpmh).CH3CN [bpmh is bis(4-pyridylmethylidene)hydrazine, C12H10N4], (I), and bis(2,9-dimethyl-1,10-phenanthroline-2N,N')copper(I) dicyanamide, [Cu(C14H12N2)2](C2N3) or [Cu(dmp)2][N(CN)2], (II), are reported. The Cu-N bond lengths and the distortion from idealized tetrahedral geometry of the dmp ligands are discussed and compared with related compounds. The bpmh molecule in (I) is pi-pi stacked with a dmp ligand at a distance of 3.4 A, rather than coordinated to the metal atom. The molecule lies across an inversion center in the crystal. In (II), the normally coordinated dicyanamide molecule is present as an uncoordinated counter-ion.

Journal Article↗
PubMed2005

Syntheses, structures, photoluminescence and theoretical studies of xanthone in crystalline resorcinarene-based inclusion complexes.

Two new crystalline resorcinarene-based xanthone inclusion complexes, CECRxanthoneMeOH (1), and HECR2 xanthone6 MeOH (2) (CECR = C-ethylcalix[4]resorcinarene, HECR = hexaethylresorcin[6]arene) have been prepared to study the relation between photophysical properties and solid-state structure. Compared with the neat crystals, the xanthone phosphorescence is severely quenched in both solids, but the lifetime is an order of magnitude larger in 2, in which xanthone occurs as a dimer, than in 1, in which it occurs as a monomer. The electronic transitions involved in the photoluminescent process, and the relation between the energy levels of host and guest and emission quenching of the guest in the supramolecular solid have been investigated by means of time-dependent density functional theory (TDDFT) calculations.

Calixarenes↗
PubMed2005

Shedding light on the structure of a photoinduced transient excimer by time-resolved diffraction.

Time-resolved single-crystal diffraction performed with synchrotron radiation shows that the 53(1) micros phosphorescent state, generated in the crystalline phase of trimeric {[3,5-(CF3)(2)Pyrazolate]Cu}(3) molecules by exposure to 355 nm of light at 17 K, is due to the formation of an excimer rather than the shortening of the intramolecular Cu...Cu distances within the trimeric units, or the formation of a continuous chain of interacting molecules. One of the intermolecular Cu...Cu distances contracts by 0.56 Angstroms from 4.018(1) to 3.46(1) Angstroms;, whereas the interplanar spacing of the trimers is reduced by 0.65 Angstroms; from 3.952(1) to 3.33(1) Angstroms. Density-functional theory calculations support the formation of a Cu...Cu bond through the intermetallic transfer of a Cu 3d electron to a molecular orbital with a large 4p contribution on the reacting Cu atoms.

Journal Article↗
PubMed2005

Synthesis, crystal structure and photoconductivity of the first [60]fullerene complex with metal diethyldithiocarbamate: {CuII(dedtc)2}2.C60.

The first molecular complex of fullerene C60 with metal dithiocarbamate, namely, {CuII(dedtc)2}2.C60(dedtc: diethyldithiocarbamate) (1) was obtained as single crystals. Butterfly-shaped CuII(dedtc)2 molecules efficiently co-crystallized with spherical fullerene molecules to form a layered structure, in which closely packed hexagonal C60 layers alternate with the layers composed of CuII(dedtc)2 dimers. The formation of the complex with C60 changes geometry and the EPR spectrum of starting CuII(dedtc)2. Magnetic susceptibility of 1 follows the Curie-Weiss law in the 300-1.9 K range with the negative Weiss constant of -2.5 K showing a weak antiferromagnetic interaction between CuII centers in the dimers. The crystals of 1 have low dark conductivity of 10(-11) S cm-1, which is consistent with a neutral ground state of the complex. Illumination of the crystals by white light increases the photocurrent by 20-50 times. The photoconductivity spectrum of 1 has a maximum at 470 nm showing that both intermolecular charge transfer between neighboring C60 molecules and photoexcitation of CuII(dedtc)2 can contribute to photogeneration of free charge carriers. The effect of a weak magnetic field with Bo<0.5 T on the photoconductivity of 1 has been found.

Journal Article↗
PubMed2005

The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffraction.

Experimental and computational methods for time-resolved (TR) diffraction now allow the determination of geometry changes on molecular excitation. The first results indicate significant changes in the interatomic distances and molecular shape on photo-excitation, but also a dependence of the induced changes on the molecular environment. Though the use of high-brightness synchrotron sources is essential, it limits the time resolution to the width of the synchrotron pulse which is currently 70-100 ps. The experiments discussed fall into two categories: (i) picosecond powder diffraction experiments on the molecular excitation to a singlet state, and (ii) microsecond experiments on the excited states of inorganic complexes. Both involve reversible processes for which a stroboscopic technique can be applied.

Journal Article↗