Acidity of uranylVI hydrate studied with first-principles molecular dynamics simulations.
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Journal Article↗
Biomedical subjects
Michael Bühl
Publications and source records attributed to Michael Bühl.
Molecular structures of arachno-decaborane derivatives 6,9-X2B8H10 (X = CH2, NH, Se) including a gas-phase electron-diffraction study of 6,9-C2B8H14.
The molecular structures of the three heterodecaboranes arachno-6,9-C2B8H14, arachno-6,9-N2B8H12, and arachno-6,9-Se2B8H10 have been determined by ab initio MO theory. In addition, the structure of arachno-6,9-C2B8H14 was experimentally determined using gas-phase electron diffraction (GED). The accuracy of all four of these structures has been confirmed by the good agreement of the (11)B chemical shifts calculated at the GIAO-MP2 level with the experimental values. A comparison of the GIAO-HF and GIAO-MP2 methods shows that for these heteroborane clusters, electron correlation effects on the computed delta((11)B) values are quite substantial and that it is necessary to go beyond the HF level in the NMR computation.
Journal Article↗
Effect of hydration on coordination properties of uranyl(VI) complexes. A first-principles molecular dynamics study.
Results from Car-Parrinello molecular dynamics simulations are reported for [UO2(OH2)5]2+, UO2(NO3)2(OH2)2, and UO2(NO3)2(eta2-tmma) (tmma = tetramethylmalonamide) in the gas phase and in aqueous solution. The distances between uranyl and neutral ligands such as water and tmma are decreased by up to 0.2 angstroms upon hydration, whereas those between uranyl and the nitrate ion are increased by up to 0.08 angstroms. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, solvation facilitates the transition of the chelating nitrate ligand to a eta1-bonding mode: the free energy of UO2(eta2-NO3)(eta1-NO3)(OH2)2 relative to the bis-chelating minimum drops from 3.9 kcal/mol in vacuo to 1.4 kcal/mol in water. Optimizations in a polarizable continuum (specifically, the conductor-like screening model in conjunction with the zero-order regular approximation and triple-zeta Slater basis sets) can qualitatively reproduce the geometrical changes from explicit hydration.
Journal Article↗
Mechanism of water exchange in aqueous uranyl(VI) ion. A density functional molecular dynamics study.
Constrained Car-Parrinello molecular dynamics simulations and thermodynamic integration have been performed for an associative pathway of water exchange between aqueous [UO2(OH2)5]2+ and bulk water. The simulated free energy of activation for this process, 6.7 kcal mol(-1), is significantly lower than that computed for a purely dissociative mechanism, 10.8 kcal mol(-1). Because the transient hexahydrate is indicated to have no chemically significant lifetime, the exchange mechanism can be classified as associative interchange.
Models, Chemical↗
Density-functional computation of 53Cr NMR chemical shifts.
53Cr chemical shifts of CrO4(2-), Cr2O7(2-), CrO3X-, CrO2X2(X = F, Cl), and Cr(CO)5L (L = CO, PF3, CHNH2, CMeNMe2) are computed, using geometries optimized with the gradient-corrected BP86 density functional, at the gauge-including atomic orbitals (GIAO)-, BPW91-, and B3LYP levels. For this set of compounds, substituent effects on delta(53Cr) are better described with the pure BPW91 functional than with B3LYP, in contrast to most other transition-metal chemical shifts studied so far. For selected cases, 53Cr NMR line widths can be rationalized in terms of electric field gradients (EFGs) computed with the BPW91 functional, but in general other factors such as molecular correlation times appear to be dominating. 53Cr chemical shifts and EFGs are predicted for CrO3, Cr(C6H6)2, Cr(C6H6)CO3, and, with reduced reliability, for Cr2(mu2-O2CH)4.
Journal Article↗
Simulation of 59Co NMR chemical shifts in aqueous solution.
59Co chemical shifts were computed at the GIAO-B3LYP level for [Co(CN)6]3-, [Co(H2O)6]3+, [Co(NH3)6]3+, and [Co(CO)4]- in water. The aqueous solutions were modeled by Car-Parrinello molecular dynamics (CPMD) simulations, or by propagation on a hybrid quantum-mechanical/molecular-mechanical Born-Oppenheimer surface (QM/MM-BOMD). Mean absolute deviations from experiment obtained with these methods are on the order of 400 and 600 ppm, respectively, over a total delta(59Co) range of about 18,000 ppm. The effect of the solvent on delta(59Co) is mostly indirect, resulting primarily from substantial metal-ligand bond contractions on going from the gas phase to the bulk. The simulated solvent effects on geometries and delta(59Co) values are well reproduced by using a polarizable continuum model (PCM), based on optimization and perturbational evaluation of quantum-mechanical zero-point corrections.
Journal Article↗
Ab initio molecular dynamics of liquid 1,3-dimethylimidazolium chloride.
Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.
Journal Article↗
Coordination environment of aqueous uranyl(VI) ion.
Water dissociation from [UO2(OH2)5]2+ is studied with Car-Parrinello molecular dynamics simulations (using the BLYP density functional) in the gas phase and in aqueous solution. Free energies, DeltaA, are estimated from pointwise thermodynamic integration using one U-O(H2) distance as a reaction coordinate. While an isomeric, four-coordinate complex, [UO2(OH2)4]2+.H2O, is more stable than the five-coordinate reactant in the gas phase (DeltaA = -2.2 kcal/mol), the former is strongly disfavored in water (DeltaA = +8.7 kcal/mol).
Journal Article↗
Molecular dynamics of a vanadate-dipeptide complex in aqueous solution.
Static geometry optimizations and Car-Parrinello molecular dynamics simulations with the BP86 density functional, as well as NMR chemical shift calculations at the GIAO-B3LYP level, have been used to assess structure, speciation, and dynamics of aqueous solutions of the vanadate-glycylglycine complex. According to the simulations, this complex should be formulated as five-coordinate, anionic [VO2(GlyGly')]- (GlyGly' = H2N-CH2-C(O)-N-CH2-CO2). The neutral conjugate acid is unstable in water, where it is deprotonated within a few picoseconds. Six-coordinate structural alternatives, [VO(OH)2(GlyGly')]-, are disfavored energetically and/or entropically. The hydration shell around [VO2(GlyGly')]- in water is characterized in terms of suitable pair correlation functions.
Glycylglycine↗
Computational study of structures and properties of metallaboranes: cobalt bis(dicarbollide).
A density functional study at the BP86/AE1 level is presented for the cobalt bis(dicarbollide) ion [3-Co-(1,2-C2B9H11)2]- (1) and selected isomers and rotamers thereof. Rotation of the two dicarbollide moieties with respect to each other is facile, as judged by the small energetic separation of the three rotamers located (within 11 kJ mol(-1)) and by the low barriers for their interconversion (at most 41 kJ mol(-1)). Among the isomers differing in carbon atom positions that contain two equivalent dicarbollide ligands, the 1,7 ("carbon apart") form [2-Co-(1,7-C2B9H11)2]- is the most stable, 121 kJ mol(-1) below 1. The electronic structure of 1 is characterized in terms of molecular orbitals, population analysis, and excitation energies from time-dependent density functional theory, relevant to UV/Vis spectroscopy. Experimental 11B NMR chemical shifts of 1 are reproduced to better than 5 ppm at the GIAO-B3LYP/II' level, and the computed delta(11B) values are only little affected by rotational averaging or the presence of a polarizable continuum. Larger such effects are found for the as-yet unknown 59Co chemical shift, for which a value in the range between -1800 and -2400 ppm is predicted. Even though the accuracy achieved for the theoretical delta(11B) values is somewhat lower than that for heteroboranes at conventional ab initio levels, the level of density functional employed can afford qualitatively reliable chemical shifts, which can be useful in assignments and structural refinements of heteroboranes containing transition metal.
Journal Article↗
Probing NMR parameters, structure and dynamics of 5-nitroimidazole derivatives. Density functional study of prototypical radiosensitizers.
The 15N chemical shifts of metronidazole (1), secnidazole (2), nimorazole (3) and tinidazole (4), radiosensitizers based on the 5-nitroimidazole motif, are reported. A detailed computational study of 1 is presented, calling special attention to the performance of various theoretical methods in reproducing the 13C and 15N data observed in solution. The most sophisticated approach involves density functional-based Car-Parrinello molecular dynamics simulations (CPMD) of 1 in aqueous solution (BP86 level) and averaging chemical shifts over snapshots from the trajectory. In the NMR calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A similarly good accord with experiment is obtained from much less involved, static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Solvent effects on delta(15N), which are of the order of up to 20 ppm, are not due to changes in geometric parameters upon solvation, but arise from the direct response of the electronic wavefunction to the presence of the solvent, which can be represented by discrete molecules and/or the dielectric bulk.
Magnetic Resonance Spectroscopy↗
Thermal effects and vibrational corrections to transition metal NMR chemical shifts.
Both zero-point and classical thermal effects on the chemical shift of transition metals have been calculated at appropriate levels of density functional theory for a number of complexes of titanium, vanadium, manganese and iron. The zero-point effects were computed by applying a perturbational approach, whereas classical thermal effects were probed by Car-Parrinello molecular dynamics simulations. The systematic investigation shows that both procedures lead to a deshielding of the magnetic shielding constants evaluated at the GIAO-B3 LYP level, which in general also leads to a downfield shift in the relative chemical shifts, delta. The effect is small for the titanium and vanadium complexes, where it is typically on the order of a few dozen ppm, and is larger for the manganese and iron complexes, where it can amount to several hundred ppm. Zero-point corrections are usually smaller than the classical thermal effect. The pronounced downfield shift is due to the sensitivity of the shielding of the metal centre with regard to the metal-ligand bond length, which increase upon vibrational averaging. Both applied methods improve the accuracy of the chemical shifts in some cases, but not in general.
Journal Article↗
Experimental investigations and ab initio studies of selenium(II) dialkanethiolates, Se(SR)2.
Selenium(II) dimethanethiolate, Se(SMe)(2), was synthesized by reaction of SeO(2) with HSMe. Basic spectroscopic data for Se(SMe)(2) and selenium(II) bis(2-methyl-2-propanethiolate), Se(S(t)Bu)(2), were recorded and interpreted with the support of ab initio calculations. Both compounds are thermodynamically unstable relatively to selenium and the corresponding disulfide. The UV/vis spectra of both compounds are qualitatively similar, the two bands being attributed to n(Se)-sigma*(Se-S) transitions. The bands at 369 and 397 cm(-1) in the IR spectra of Se(SMe)(2) and Se(S(t)Bu)(2), respectively, are assigned to nu(as)(SeS(2)). The (77)Se NMR shifts of Se(SMe)(2)(784 ppm) and Se(S(t)Bu)(2)(556 ppm) differ substantially from each other and show positive temperature gradients. Calculations at the GIAO-HF/962+(d) level reproduced the difference of the (77)Se NMR chemical shifts between Se(SMe)(2) and Se(S(t)Bu)(2). At the same level, the effect of conformational changes on (77)Se shifts were studied for Se(SMe)(2). In the solid state Se(SMe)(2) forms long intermolecular SeS contacts while Se(S(t)Bu)(2) does not. Both compounds exhibit anti-conformations of the methyl and tert-butyl groups with respect to the SeS(2) plane. MP2/LANL2DZ(d) geometry optimizations, single point energy and frequency calculations performed for Se(SMe)(2) show, that syn- (C(s)) and anti-conformers (C(2)) represent minima on the potential energy surface, the latter being by 8 kJ mol(-1) lower in energy than the former. Both conformers are stabilized by intramolecular pi-type n(S(1))-sigma*(Se-S(2)) orbital interactions. The energy of the transition state for the mutual conversion of the two conformers was calculated to be 31 kJ mol(-1) above that of the syn conformer, allowing a rapid interconversion of the two conformers at room temperature. Intermolecular interactions between Se(SMe)(2) molecules were also studied by means of calculations at the MP2/LANL2DZ(d) level. For Se(S(t)Bu)(2) MP2/LANL2DZ(d) geometry optimizations and single point energy calculations revealed a C(2)-symmetric anti- and a C(1) symmetric syn-conformer, the latter being 21 kJ mol(-1) higher in energy than the former. Se(SMe)(2) and Se(S(t)Bu)(2) exchange thiolate groups with other selenium(II) dithiolates, tellurium(II) dithiolates and with thiols, if catalytic amounts of p-CH(3)C(6)H(4)SO(3)H are added.
Journal Article↗
Density functional study of valence trapping in a mixed-valent dimanganese complex.
Density functional calculations are reported for the linked system [(Fulv)[Mn(CO)(2)](2)(mu-dppm)] in the neutral and singly and doubly charged states. The neutral system and dication are characterized by well-localized valence states involving two Mn(II) and Mn(I) centers, respectively. At the BP86/AE1 level, the electronic structure of the monocation is that of a delocalized mixed-valence species. At the B3LYP/AE1 level, the spin density of the unpaired electron is largely localized on one Mn atom, in accord with the formulation of a trapped-valence ground state (Atwood, C. G.; Geiger, W. E. J. Am. Chem. Soc. 2000, 122, 5477). The qualitative IR pattern of the CO stretching vibrations is well reproduced at the B3LYP level, supporting the empirical charge distribution parameter employed for the interpretation of the IR spectra.
Computer Simulation↗
Rovibrational corrections to transition metal NMR shielding constants.
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Journal Article↗
Peroxovanadate imidazole complexes as catalysts for olefin epoxidation: density functional study of dynamics, 51V NMR chemical shifts, and mechanism.
A density functional study of [VO(O(2))(2)(Im)](-) (1, Im = imidazole) is presented, calling special attention to effects of dynamics and solvation on the (51)V chemical shift. According to Car-Parrinello molecular dynamics simulations, rotation of the Im ligand can be fast in the gas phase, but is more hindered in aqueous solution. In the latter, bonding between Im and V is reinforced, and dynamic averaging of GIAO-B3LYP magnetic shieldings affords a gas-to-liquid shift of ca. -100 ppm for delta((51)V). A complete catalytic cycle has been characterized for olefin epoxidation mediated by 1, using H(2)O(2) as oxidant. The rate-determining step is indicated to be initial oxygen atom transfer from 1 to the substrate via a spiro-like transition state. Substituent effects on this barrier are examined, and a significant decrease (by 2-6 kcal/mol) is revealed upon removal of the Im proton or upon complexation with a H-bond acceptor. Implications for the mechanism of the oxidative chemistry of vanadium-dependent haloperoxidases and requirements for prospective biomimetic analogues are discussed.
Journal Article↗
Synthesis, structure, theoretical studies, and Ligand exchange reactions of monomeric, T-shaped arylpalladium(II) halide complexes with an additional, weak agostic interaction.
A series of monomeric arylpalladium(II) complexes LPd(Ph)X (L = 1-AdPtBu2, PtBu3, or Ph5FcPtBu2 (Q-phos); X = Br, I, OTf) containing a single phosphine ligand have been prepared. Oxidative addition of aryl bromide or aryl iodide to bis-ligated palladium(0) complexes of bulky, trialkylphosphines or to Pd(dba)2 (dba = dibenzylidene acetone) in the presence of 1 equiv of phosphine produced the corresponding arylpalladium(II) complexes in good yields. In contrast, oxidative addition of phenyl chloride to the bis-ligated palladium(0) complexes did not produce arylpalladium(II) complexes. The oxidative addition of phenyl triflate to PdL2 (L = 1-AdPtBu2, PtBu3, or Q-phos) also did not form arylpalladium(II) complexes. The reaction of silver triflate with (1-AdPtBu2)Pd(Ph)Br furnished the corresponding arylpalladium(II) triflate in good yield. The oxidative addition of phenyl bromide and iodide to Pd(Q-phos)2 was faster than oxidative addition to Pd(1-AdPtBu2)2 or Pd(PtBu3)2. Several of the arylpalladium complexes were characterized by X-ray diffraction. All of the arylpalladium(II) complexes are T-shaped monomers. The phenyl ligand, which has the largest trans influence, is located trans to the open coordination site. The complexes appear to be stabilized by a weak agostic interaction of the metal with a ligand C-H bond positioned at the fourth-coordination site of the palladium center. The strength of the Pd.H bond, as assessed by tools of density functional theory, depended upon the donating properties of the ancillary ligands on palladium.
Ferrous Compounds↗
Density functional computation of 49Ti NMR chemical shifts.
49Ti chemical shifts of TiX4 (X = Cl, Br, F), TiClnMe(4-n) (n = 0-3), Ti(C5H5)2X2 (X = F, Cl, Br) and Ti(CO)6(2-) were computed, using geometries optimized with the gradient-corrected BP86 density functional, at the GIAO (gauge-including atomic orbitals)-Hartree-Fock, BPW91, and B3LYP levels. For this set of compounds, substituent effects on delta(49Ti) are reasonably well described with all methods considered; judged from mean absolute deviations from experiment, B3LYP performs best. Zero-point corrections to the delta(49Ti) values, evaluated from a perturbational approach based on vibrationally averaged effective geometries, turn out to be fairly small. Electric field gradients computed with the B3LYP functional do not correlate with trends in 49Ti NMR linewidths. Attempts are reported to correlate the delta(49Ti) values of Ti[YC(O)CHC(O)Y]2Cl2 (Y = H, Me, CF3, CN, F, Cl and Br) with the rate-limiting propagation barrier for ethylene polymerization using catalysts derived from these precursors.
Algorithms↗