Biomedical subjects

Simon Petrie

Publications and source records attributed to Simon Petrie.

11 recordsLinked to original sources

PubMed2006

Mixed-metal cluster chemistry. 29. Core expansion and ligand-driven metal exchange at group 6-iridium clusters.

Reactions of the tetrahedral clusters MoIr3(mu-CO)3(CO)8(eta-L) (L = C5HMe4, C5Me5) with the carbonylmetalate anions [Mo(CO)3(eta-L)]- afford the trigonal bipyramidal clusters Mo2Ir3(mu3-H)(mu-CO)2(CO)9(eta-L)2 (L = C5HMe4 (3c), 74%; L = C5Me5 (3d), 55%) in which the group 6 metal atoms occupy the apexes; reaction of the cyclopentadienylmolybdenum-containing analogues or their cyclopentadienyltungsten-containing homologues failed to afford analogous products. Reactions of MIr3(mu-CO)3(CO)8(eta-C5H5) (M = Mo, W) with [M(CO)3(eta-L)]- (L = C5HMe4, C5Me5) afford the core-expanded heteroapex clusters M2Ir3(mu3-H)(mu-CO)2(CO)9(eta-C5H5)(eta-L) (M = Mo, L = C5HMe4 (5c), 9%, L = C5Me5 (5d), 4%; M = W, L = C5Me5 (6d), 5%) in low yield, together with the homoapex clusters M2Ir3(mu3-H)(mu-CO)2(CO)9(eta-L)2 (M = Mo, L = C5HMe4 (3c), 81%, L = C5Me5 (3d), 60%; M = W, L = C5Me5 (4d), 5%) in much higher yield for the Mo-containing examples. The identities of clusters 3c,d, 4d, and 5c,d have been confirmed by single-crystal X-ray diffraction studies, with the same disposition of ligands about the trigonal bipyramidal cluster cores being observed in each case, a ligand arrangement that has been examined by complementary density functional theory studies. While cluster 5d is accessible as above, no reaction is observed from MoIr3(mu-CO)3(CO)8(eta-C5Me5) and [M(CO)3(eta-C5H5)]-. Treating MoIr3(mu-CO)3(CO)8(eta-C5H5) with 1 equiv of [M(CO)3(eta-C5Me5)]- affords 5d as the major product, a further 1 equiv affording some MoIr3(mu-CO)3(CO)8(eta-C5Me5) and a third 1 equiv giving a good yield of 3d. This is consistent with reaction proceeding by apex fragment addition, followed by apex fragment elimination, and finally a further apex fragment addition, the homometallic incoming apexes being distinguished from the departing vertices by their highly methylated cyclopentadienyl ligands. Spectroscopic data suggest that the electron density at these disparate-metal-containing cluster cores is tunable by progressive (conceptual) cyclopentadienyl alkylation.

Journal Article↗

PubMed2006

Extending, and repositioning, a thermochemical ladder: high-level quantum chemical calculations on the sodium cation affinity scale.

High-level ab initio quantum chemical calculations, at the CP-dG2thaw level of theory, are reported for coordination of Na+ to a wide assortment of small organic and inorganic ligands. The ligands range in size from H to C6H6, and include 22 of the ligands for which precise relative sodium ion binding free energies have been determined by recent Fourier transform ion cyclotron resonance and guided ion beam studies. Agreement with the relative experimental values is excellent (+/-1.1 kJ mol(-1)), and agreement with the absolute scale (obtained when these relative values are pegged to the CH3NH2 "anchor" value measured in a high-pressure mass spectrometric study) is only marginally poorer, with CP-dG2thaw values exceeding the absolute experimental DeltaG(298) values by an average of 2.1 kJ mol(-1). The excellent agreement between experiment and the CP-dG2thaw technique also suggests that the additional 97 ligands surveyed here (which, in many cases, are not readily susceptible to laboratory investigation) can also be reliably fitted to the existing experimental scale. However, while CP-dG2thaw and the experimental ladder are in close accord, a small set of higher level ab initio calculations on sodium ion/ligand complexes (including several values obtained here using the W1 protocol) suggests that the CP-dG2thaw values are themselves too low by approximately 2.5 kJ mol(-1), thereby implying that the accepted laboratory values are typically 4.6 kJ mol(-1) too low. The present work also highlights the importance of Na+/ligand binding energy determinations (whether by experimental or theoretical approaches) on a case-by-case basis: trends in increasing binding energy along homologous series of compounds are not reliably predictable, nor are binding site preferences or chelating tendencies in polyfunctional compounds.

Fourier Analysis↗

PubMed2005

CH2CHOH2+ + PN: a proton-transfer triple play.

Quantum chemical calculations are used to explore the proton-transfer reactivity of O-protonated vinyl alcohol, CH2CHOH2+, with phosphorus nitride, PN. This reaction is relevant to the chemical evolution of interstellar clouds, since O-protonated vinyl alcohol has been postulated (and tentatively identified) as a product of the association reaction between interstellar H3O+ and C2H2, while PN is the most widespread and abundant phosphorus-containing molecule seen in astrophysical environments. Furthermore, the reaction exhibits an unusual mechanistic feature, namely, an extended "proton-transport catalysis" mechanism, which we characterize here as a "proton-transfer triple play". The reaction proceeds initially by proton transfer from CH2CHOH2+ to PN, then from PNH+ to CH2CHOH, and finally from CH3CHOH+ to PN, where the emphasized atom indicates the resultant site of protonation/deprotonation. Thus, the ultimate overall bimolecular proton-transfer reaction is expected to occur as CH2CHOH2+ + PN --> CH3CHO + PNH+; that is, the apparent favored product channel exhibits not only proton transfer but also keto/enol tautomerization. The triple-play mechanism can be rationalized in terms of the proton affinities of vinyl alcohol, acetaldehyde, and phosphorus nitride, which here are satisfactorily reproduced by high-level ab initio calculations. Other neutrals with a proton affinity appropriate for the possible triple-play mechanism converting CH2CHOH2+ to CH3CHO are also identified, with a view to encouraging experimental investigation of this mechanism.

Journal Article↗

PubMed2005

Magnesium monocationic complexes: a theoretical study of metal ion binding energies and gas-phase association kinetics.

Bond dissociation energies (BDEs) for complexes of ground state Mg+ (2S) with several small oxygen- and nitrogen-containing ligands (H2O, CO, CO2, H2CO, CH3OH, HCOOH, H2CCO, CH3CHO, c-C2H4O, H2CCHOH, CH3CH2OH, CH3OCH3, NH3, HCN, H2CNH, CH3NH2, CH3CN, CH3CH2NH2, (CH3)2NH, H2NCN, and HCONH2) have been calculated at the CP-dG2thaw level of theory. These BDE values, as well as counterpoise-corrected MP2(thaw)/6-311+G(2df,p) calculations on the Mg+ complexes of several larger ligands, augment and complement existing experimental or theoretical determinations of gas-phase Mg+/ligand bond strengths. The reaction kinetics of complex formation are also investigated via variational transition state theory (VTST) calculations using the computed ligand and molecular ion parameters. Radiative association rate coefficients for most of these systems increase by approximately 1 order of magnitude with every 3-fold reduction in temperature from 300 to 10 K. Several of the largest molecules surveyed-notably, CH3COOH, (CH3)2CO, and CH3CH2CN-exhibit comparatively efficient radiative association with Mg+ (k(RA) > or = 1.0 x 10(-10) cm3 molecule(-1) s(-1)) at temperatures as high as 100 K, implying that these processes may have a considerable influence on the metal ion chemistry of warm molecular astrophysical environments known to contain these potential ligands. Our calculations also identify the infrared chromophoric brightness of various functional groups as a significant factor influencing the efficiency of the radiative association process.

Journal Article↗

PubMed2004

On the mechanism of dioxygen formation from a di-mu-oxo-bridged manganese dinuclear complex.

Density functional theory (DFT) calculations, using the Becke-Perdew gradient-corrected functional with a triple-zeta-plus-polarization basis set, have been used to characterize the [(H(2)O)(H(3)N)(3)Mn(mu-O)(2)Mn(NH(3))(3)(OH(2))](q)(+) (q = 2-5) complexes. This structure has been proposed as a possible model for the oxygen-releasing site of the photosystem II (PSII) reaction center. We have performed full optimizations to locate stationary points in various spin states for each of the +2 to +5 charge states. Our calculations indicate that O(2) release from the vacuum-phase +5 charge state complex is barrier inhibited, in contrast to the results of a recent DFT study. We report several new di-mu-oxo-bridged stationary points with spin multiplicities of S = (1)/(2), (3)/(2), and (5)/(2) and effective metal oxidation states of Mn(IV)Mn(V) for the +5 charge state. Finally, calculations employing the 'conductorlike screening model' (COSMO), to address the inclusion of solvent effects, indicate that dissociative O(2) release from the +5 charge state model complex is inhibited by a major barrier and is therefore apparently highly disfavored.

Journal Article↗

PubMed2004

DFT and metal-metal bonding: a dys-functional treatment for multiply charged complexes?

Density functional theory (DFT) calculations are reported for 16 binuclear transition-metal complexes. Structural motifs studied include face-shared and edge-shared bioctahedra, carboxylate-bridged "paddlewheel" complexes, and nonbridged dimers possessing direct metal-metal bonds. Most of these structure types are represented both by multiply charged (tri- and tetra-anionic, and tetracationic) and by neutral or singly charged examples. Geometry optimizations for these species, in the vacuum phase, use the "broken-symmetry" approach coupled with nine different DFT methods. We find a clear dichotomy in the performance of different DFT approaches. For the eight neutral or singly charged complexes, orthodox gradient-corrected DFT methods such as BP and PBE perform generally very well in reproducing in vacuo the complex geometries obtained from X-ray crystallographic studies. In contrast, these orthodox approaches fail to reliably mimic the crystalline geometries for more highly charged complexes such as Mo(2)Cl(9)(3-), Cr(2)(CH(3))(8)(4-), and Rh(2)(NCCH(3))(10)(4+). Much closer agreement with experimental condensed-phase structures for the multiply charged dinuclear complexes is seen for two "local-density-approximation" approaches, X alpha and VWN, and for VWN+B-LYP, an unorthodox combination of the VWN local and B-LYP nonlocal density functionals. The very good performance of the latter approaches arises from an essentially fortuitous cancellation of errors: while the generally overbinding nature of these approaches suggests that they will not reliably describe true gas-phase structures, this overbinding compensates very well for the coulombic distortion expected when complexes are removed from the charge-stabilizing environment of the crystalline or solvated state. We recommend that, as an alternative to the (computationally expensive) incorporation of solvent-field corrections, VWN+B-LYP is the preferred method for structural characterization of triply or more highly charged dinuclear complexes, while orthodox approaches such as PBE perform best for neutral or mildly charged complexes.

Journal Article↗

PubMed2003

Cl(3)V(mu-S(CH(3))(2))(3)VCl(3)(2)(-): a first-row, face-shared bioctahedral complex with multiple metal-metal bonding.

Density functional theory calculations have been used to investigate the structure and bonding of the d(3)d(3) bioctahedral complexes X(3)V(mu-S(CH(3))(2))(3)VX(3)(2)(-) (X = F(-), Cl(-), OH(-), SH(-), NH(2)(-)). According to geometry optimizations using the broken-symmetry approach and the VWN+B-LYP combination of density functionals, the halide-terminated complexes have a V-V bond order of approximately 2, while complexes featuring OH(-), SH(-), or NH(2)(-) as terminal ligands exhibit full triple bonding between the vanadium atoms. The tendency toward triple bonding in the latter complexes is consistent with an increased covalency of the vanadium-ligand bonds, and the influence of bond covalency is apparent also in the tendency for V-V bond elongation in the complexes with OH(-) and NH(2)(-) terminal ligands. Detailed examination of the composition of molecular orbitals in all of the thioether-bridged V(II) complexes substantiates the conclusion that the strong antiferromagnetic coupling which we have determined for these complexes (-J > 250 cm(-)(1)) is due to direct bonding between metal atoms rather than superexchange through the bridging ligands. As such, these V(II) complexes comprise the first apparent examples of multiple metal-metal bonding in first-transition-row, face-shared dinuclear complexes and are therefore of considerable structural and synthetic interest.

Journal Article↗

PubMed2002

Factors affecting metal-metal bonding in the face-shared d(3)d(3) bioctahedral dimer systems, MM'Cl(9)(5-) (M, M' = V, Nb, Ta).

Density functional theory (DFT) calculations have been used to investigate the d(3)d(3) bioctahedral complexes, MM'Cl(9)(5-), of the vanadium triad. Broken-symmetry calculations upon these species indicate that the V-containing complexes have optimized metal-metal separations of 3.4-3.5 A, corresponding to essentially localized magnetic electrons. The metal-metal separations in these weakly coupled dimers are elongated as a consequence of Coulombic repulsion, which profoundly influences (and destabilizes) the gas-phase structures for such dimers; nevertheless, the intermetallic interactions in the V-containing dimers involve significantly greater metal-metal bonding character than in the analogous Cr-containing dimers. These observations all show good agreement with existing experimental (solid state) results for the chloride-bridged, face-shared dimers V(2)Cl(9)(5-) and V(2)Cl(3)(thf)(6)(+). In contrast to the V-containing dimers, complexes featuring only Nb and Ta have much shorter intermetallic distances (approximately 2.4 A) consistent with d-electron delocalization and formal metal-metal triple bond formation; again, good agreement is found with available experimental data. Calculations on the complexes V(2)(mu-Cl)(3)(dme)(6)(+), Nb(2)(mu-dms)(3)Cl(6)(2-), and Ta(2)(mu-dms)(3)Cl(6)(2-), which are closely related to compounds for which crystallographic structural data exist, have been pursued and provide an insight into the intermetallic interactions in the experimentally characterized complexes. Analysis of the contributions from d-orbital overlap (E(ovlp)) stabilization, as well as spin polarization (exchange) stabilization of localized d electrons (E(spe)), has also been attempted for the MM'Cl(9)(5-) dimers. While E(ovlp) clearly dominates over E(spe) as a stabilizing factor in those dimers containing only Nb and Ta metal atoms, detailed assessment of the competition between E(ovlp) and E(spe) for V-containing dimers is obstructed by the instability of triply bonded V-containing dimers against Coulombic explosion. On the basis of the periodic trends in E(ovlp) versus E(spe), the V-triad dimers have a greater propensity for metal-metal bonding than do their Cr-triad or Mn-triad counterparts.

Journal Article↗

PubMed2002

Mixed-metal cluster chemistry. 19. Crystallographic, spectroscopic, electrochemical, spectroelectrochemical, and theoretical studies of systematically varied tetrahedral group 6-iridium clusters.

A systematically varied series of tetrahedral clusters involving ligand and core metal variation has been examined using crystallography, Raman spectroscopy, cyclic voltammetry, UV-vis-NIR and IR spectroelectrochemistry, and approximate density functional theory, to assess cluster rearrangement to accommodate steric crowding, the utility of metal-metal stretching vibrations in mixed-metal cluster characterization, and the possibility of tuning cluster electronic structure by systematic modification of composition, and to identify cluster species resultant upon electrochemical oxidation or reduction. The 60-electron tetrahedral clusters MIr(3)(CO)(11-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (5), C(5)HMe(4) (6), C(5)Me(5) (7); M = W, Cp = C(5)H(4)Me, x = 1 (13), x = 2 (14)] and M(2)Ir(2)(CO)(10-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (8), C(5)HMe(4) (9), C(5)Me(5) (10); M = W, Cp = C(5)H(4)Me, x = 1 (15), x = 2 (16)] have been prepared. Structural studies of 7, 10, and 13 have been undertaken; these clusters are among the most sterically encumbered, compensating by core bond lengthening and unsymmetrical carbonyl dispositions (semi-bridging, semi-face-capping). Raman spectra for 5, 8, WIr(3)(CO)(11)(eta(5)-C(5)H(4)Me) (11), and W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(4)Me)(2) (12), together with the spectrum of Ir(4)(CO)(12), have been obtained, the first Raman spectra for mixed-metal clusters. Minimal mode-mixing permits correlation between A(1) frequencies and cluster core bond strength, frequencies for the A(1) breathing mode decreasing on progressive group 6 metal incorporation, and consistent with the trend in metal-metal distances [Ir-Ir < M-Ir < M-M]. Cyclic voltammetric scans for 5-15, MoIr(3)(CO)(11)(eta(5)-C(5)H(5)) (1), and Mo(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (3) have been collected. The [MIr(3)] clusters show irreversible one-electron reduction at potentials which become negative on cyclopentadienyl alkyl introduction, replacement of molybdenum by tungsten, and replacement of carbonyl by phosphine. These clusters show two irreversible one-electron oxidation processes, the easier of which tracks with the above structural modifications; a third irreversible oxidation process is accessible for the bis-phosphine cluster 14. The [M(2)Ir(2)] clusters show irreversible two-electron reduction processes; the tungsten-containing clusters and phosphine-containing clusters are again more difficult to reduce than their molybdenum-containing or carbonyl-containing analogues. These clusters show two one-electron oxidation processes, the easier of which is reversible/quasi-reversible, and the more difficult of which is irreversible; the former occur at potentials which increase on cyclopentadienyl alkyl removal, replacement of tungsten by molybdenum, and replacement of phosphine by carbonyl. The reversible one-electron oxidation of 12 has been probed by UV-vis-NIR and IR spectroelectrochemistry. The former reveals that 12(+) has a low-energy band at 8000 cm(-1), a spectrally transparent region for 12, and the latter reveals that 12(+) exists in solution with an all-terminal carbonyl geometry, in contrast to 12 for which an isomer with bridging carbonyls is apparent in solution. Approximate density functional calculations (including ZORA scalar relativistic corrections) have been undertaken on the various charge states of W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (4). The calculations suggest that two-electron reduction is accompanied by W-W cleavage, whereas one-electron oxidation proceeds with retention of the tetrahedral core geometry. The calculations also suggest that the low-energy NIR band of 12(+) arises from a sigma(W-W) --> sigma*(W-W) transition.

Journal Article↗

PubMed2002

Magnetic coupling and intermetallic electron transfer in the heterodinuclear bioctahedral complexes MW(III)Cl(9)(n-) (M = V(II), Cr(III), Mn(IV)): tweaking the balance between ferromagnetism and antiferromagnetism.

Density functional theory (DFT) calculations have been used to investigate the effect of intermetallic electron transfer on the mode of magnetic coupling in the face-shared bimetallic complexes MWCl(9)(n-) (M = V, Cr, Mn; all with a nominal d(3) valence electronic configuration on each metal atom). These calculations illustrate a simple rule: when the oxidation state of M is lower than that of W, antiferromagnetic coupling is preferred, while ferromagnetism (via crossed exchange pathways) is favored when M has the higher oxidation state. This underlying trend in intermetallic interactions is seen to depend on the interplay among ligand field splitting, spin polarization splitting of alpha- and beta-spin orbitals, and the relative energies of the M and W valence d orbitals, and is mirrored in the results seen in a wider survey of mixed-metal, face-shared complexes.

Journal Article↗

PubMedDate not supplied

Ions in space.

We review the detection history, observation, distribution, and reactivity of molecular ions in extraterrestrial space, with particular (though not exclusive) reference to interstellar monocations. The diversity of interstellar ion chemistry is highlighted with reaction examples, drawn from the authors' own laboratories and elsewhere, and attempt to provide an overview of this broad and increasingly divergent field. Emphasis is given to the role of ions in the synthesis of molecules, including their ability to catalyze the transformation of neutral molecules.

Journal Article↗