Biomedical subjects

Richard P Muller

Publications and source records attributed to Richard P Muller.

9 recordsLinked to original sources

PubMed2006

Mechanism of direct molecular oxygen insertion in a palladium(II)-hydride bond.

The mechanism of the direct insertion of molecular oxygen into a palladium hydride bond has been elucidated using quantum mechanics (B3LYP/LACVP** with the PBF continuum solvent model). The key step is found to be the abstraction of the hydrogen atom resulting in the formation of a PdI/HO2 (triplet) radical pair, which then proceeds to form a singlet palladium hydroperoxo species. Potential palladium(0) pathways were explored and were found to be inaccessible. The results are in agreement with recent experimental results and are consistent with our previously predicted mechanism for an analogue system.

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PubMed2006

Optimized effective potential from a correlated wave function: optimized effective potential-generalized valence bond (OEP-GVB).

The optimized effective potential (OEP) method allows orbital-dependent functionals to be used in density functional theory. Traditionally the orbital-dependent functional of interest has been the Hartree-Fock energy, leading to exact exchange density functional theory. Here we present results that use a generalized valence-bond (GVB) wave function, a multiconfigurational wave function that includes static correlation and dissociates to the proper limits. We demonstrate the effectiveness of the OEP-GVB method by showing the dissociation of H2 and the excitation spectrum of He.

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PubMed2005

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems.

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with R(e) and D(e) within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions.

Binding Sites↗

PubMed2004

Hydrogen storage in LiAlH4: predictions of the crystal structures and reaction mechanisms of intermediate phases from quantum mechanics.

We use the density functional theory and x-ray and neutron diffraction to investigate the crystal structures and reaction mechanisms of intermediate phases likely to be involved in decomposition of the potential hydrogen storage material LiAlH(4). First, we explore the decomposition mechanism of monoclinic LiAlH(4) into monoclinic Li(3)AlH(6) plus face-centered cubic (fcc) Al and hydrogen. We find that this reaction proceeds through a five-step mechanism with an overall activation barrier of 36.9 kcal/mol. The simulated x ray and neutron diffraction patterns from LiAlH(4) and Li(3)AlH(6) agree well with experimental data. On the other hand, the alternative decomposition of LiAlH(4) into LiAlH(2) plus H(2) is predicted to be unstable with respect to that through Li(3)AlH(6). Next, we investigate thermal decomposition of Li(3)AlH(6) into fcc LiH plus Al and hydrogen, occurring through a four-step mechanism with an activation barrier of 17.4 kcal/mol for the rate-limiting step. In the first and second steps, two Li atoms accept two H atoms from AlH(6) to form the stable Li-H-Li-H complex. Then, two sequential H(2) desorption steps are followed, which eventually result in fcc LiH plus fcc Al and hydrogen: Li(3)AlH(6)(monoclinic)-->3 LiH(fcc)+Al(fcc)+3/2 H(2) is endothermic by 15.8 kcal/mol. The dissociation energy of 15.8 kcal/mol per formula unit compares to experimental enthalpies in the range of 9.8-23.9 kcal/mol. Finally, we explore thermal decomposition of LiH, LiH(s)+Al(s)-->LiAl(s)+12H(2)(g) is endothermic by 4.6 kcal/mol. The B32 phase, which we predict as the lowest energy structure for LiAl, shows covalent bond characters in the Al-Al direction. Additionally, we determine that transformation of LiH plus Al into LiAlH is unstable with respect to transformation of LiH through LiAl.

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PubMed2004

Mechanism of the Stoddart-Heath bistable rotaxane molecular switch.

We use quantum mechanics to characterize the structure and current-voltage performance of the Stoddart-Heath rotaxane-based programmable electronic switch. We find that the current when the ring is on the DNP is 37-58 times the current when the ring is on the TTF, in agreement with experiment (ratio of 10-100). This establishes the basis for iterative experimental-theoretical efforts to optimize systems for molecule-based electronics which we illustrate by predicting the effect of adding a group such as CN to the rotaxane.

Journal Article↗

PubMed2004

Mechanism of homogeneous Ir(III) catalyzed regioselective arylation of olefins.

The mechanism of hydroarylation of olefins by a homogeneous Ph-Ir(acac)(2)(L) catalyst is elucidated by first principles quantum mechanical methods (DFT), with particular emphasis on activation of the catalyst, catalytic cycle, and interpretation of experimental observations. On the basis of this mechanism, we suggest new catalysts expected to have improved activity. Initiation of the catalyst from the inert trans-form into the active cis-form occurs through a dissociative pathway with a calculated DeltaH(0 K)() = 35.1 kcal/mol and DeltaG(298 K)() = 26.1 kcal/mol. The catalytic cycle features two key steps, 1,2-olefin insertion and C-H activation via a novel mechanism, oxidative hydrogen migration. The olefin insertion is found to be rate determining, with a calculated DeltaH(0 K)() = 27.0 kcal/mol and DeltaG(298 K)() = 29.3 kcal/mol. The activation energy increases with increased electron density on the coordinating olefin, as well as increased electron-donating character in the ligand system. The regioselectivity is shown to depend on the electronic and steric characteristics of the olefin, with steric bulk and electron withdrawing character favoring linear product formation. Activation of the C-H bond occurs in a concerted fashion through a novel transition structure best described as an oxidative hydrogen migration. The character of the transition structure is seven coordinate Ir(V), with a full bond formed between the migrating hydrogen and iridium. Several experimental observations are investigated and explained: (a) The nature of L influences the rate of the reaction through a ground-state effect. (b) The lack of beta-hydride products is due to kinetic factors, although beta-hydride elimination is calculated to be facile, all further reactions are kinetically inaccessible. (c) Inhibition by excess olefin is caused by competitive binding of olefin and aryl starting materials during the catalytic cycle in a statistical fashion. On the basis of this insertion-oxidative hydrogen transfer mechanism we suggest that electron-withdrawing substituents on the acac ligands, such as trifluoromethyl groups, are good modifications for catalysts with higher activity.

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PubMed2002

Computational insights on the challenges for polymerizing polar monomers.

Taking Pd di-imine catalysts as an example, we use first principles density functional theory (B3LYP/6-31G) to investigate the chain propagation steps for polymerization of polar monomers. We start with the complex formed from insertion of ethylene into the polymer chain and consider insertion into the Pd-C bond for each of four polar monomers: methyl acrylate, vinyl acetate, vinyl chloride, and acrylonitrile. We find 2,1-insertion is favored in each case (by 3 to 5 kcal/mol), resulting in a product with a strong interaction of the polar group for the growing polymer chain with the metal. Next, we insert another unit of the same polar monomer or an ethylene unit (except for acrylonitrile). We optimize the structures for all important intermediates and transition states using a continuum dielectric to account for solvation effects. These studies pinpoint the critical difficulties in designing catalysts to polymerize polar monomers.

Journal Article↗

PubMed2002

An NMR and quantum-mechanical investigation of tetrahydrofuran solvent effects on the conformational equilibria of 1,4-butanedioic acid and its salts.

Vicinal proton-proton NMR couplings have been used to compare the influences of water and tetrahydrofuran (THF) as solvents on the conformational equilibria of 1,4-butanedioic (succinic) acid and its mono- and dianionic salts. An earlier NMR investigation (Lit, E. S.; Mallon, F. K.; Tsai, H. Y.; Roberts, J. D. J. Am Chem. Soc. 1993, 115, 9563-9567) showed that, in water, the conformational preferences for the gauche conformations for butanedioic acid and its monoanion and dianion were, respectively, approximately 84%, 66%, and 43%, essentially independent of the nature of the cation or concentration. We now report the corresponding gauche percentages calculated in the same way for 0.05 M solutions in THF to be 66%, 90-100%, and 46-64%. Substantial evidence was adduced for the rotational angle between the substituents in the monoanion being approximately 70 degrees. The positions of conformational equilibria of the salts in THF, particularly of the dianion, were found to be rather insensitive to concentration and temperature, but more sensitive to the amount of water present. Ab initio quantum-mechanical calculations for 1,4-butanedioate dianion indicate that, as expected for the gas phase, the trans conformation of the dianion should be heavily favored over the gauche, but, in both THF and water, the gauche conformation is calculated to predominate with rotational angles substantially less than 60 degrees. This conclusion is, in fact, generally consistent with the experimental vicinal proton couplings, which are wholly inconsistent with the trans conformation.

Journal Article↗

PubMed2002

The gas phase reaction of singlet dioxygen with water: a water-catalyzed mechanism.

Stimulated by the recent surprising results from Wentworth et al. [Wentworth, A. D., Jones, L. H., Wentworth, P., Janda, K. D. & Lerner, R. A. (2000) Proc. Natl. Acad. Sci. USA 97, 10930-10935] that Abs efficiently catalyze the conversion of molecular singlet oxygen ((1)O(2)) plus water to hydrogen peroxide (HOOH), we used quantum chemical methods (B3LYP density functional theory) to delineate the most plausible mechanisms for the observed efficient conversion of water to HOOH. We find two reasonable pathways. In Pathway I, (i) H(2)O catalyzes the reaction of (1)O(2) with a second water to form HOOOH; (ii) two HOOOH form a dimer, which rearranges to form the HOO-HOOO + H(2)O complex; (iii) HOO-HOOO rearranges to HOOH-OOO, which subsequently reacts with H(2)O to form H(2)O(4) + HOOH; and (iv) H(2)O(4) rearranges to the cyclic dimer (HO(2))(2), which in turn forms HOOH plus (1)O(2) or (3)O(2). Pathway II differs in that step ii is replaced with the reaction between HOOOH and (1)O(2), leading to the formation of HOO-HOOO. This then proceeds to similar products. For a system with (18)O H(2)O, Pathway I leads to a 2.2:1 ratio of (16)O:(18)O in the product HOOH, whereas Pathway II leads to 3:1. These ratios are in good agreement with the 2.2:1 ratio observed in isotope experiments by Wentworth et al. These mechanisms lead to two HOOH per initial (1)O(2) or one, depending on whether the product of step iv is (1)O(2) or (3)O(2), in good agreement with the experimental result of 2.0. In addition to the Ab-induced reactions, the hydrogen polyoxides (H(2)O(3) and H(2)O(4)) formed in these mechanisms and their decomposition product polyoxide radicals (HO(2), HO(3)) may play a role in combustion, explosions, atmospheric chemistry, and the radiation chemistry in aqueous systems.

Antibodies, Catalytic↗