New pseudospectral algorithms for electronic structure calculations: Length scale separation and analytical two-electron integral corrections

Greeley, Burnham H.; Russo, Thomas V.; Mainz, Daniel T.; Friesner, Richard A.; Langlois, Jean‐Marc; Goddard, William A.; Donnelly, Robert E.; Ringnalda, Murco N.

doi:10.1063/1.467520

Cited by 135 publications

(119 citation statements)

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“…Vibrational frequencies of a single organic molecule were calculated using density functional theory (DFT) approaches to quantum mechanical (QM) models of bond energies, performed using Jaguar 7.0 (Greeley 1994). Calculations were carried out at the B3LYP/6-311G * * level.…”

Section: Ab Initio Modelingmentioning

confidence: 99%

Accretion and Preservation of D-Rich Organic Particles in Carbonaceous Chondrites: Evidence for Important Transport in the Early Solar System Nebula

Rémusat

Guan

Wang

et al. 2010

ApJ

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We have acquired NanoSIMS images of the matrices of CI, CM, and CR carbonaceous chondrites to study, in situ, the organic matter trapped during the formation of their parent bodies. D/H ratio images reveal the occurrence of D-rich hot spots, constituting isolated organic particles. Not all the organic particles are D-rich hot spots, indicating that at least two kinds of organic particles have been accreted in the parent bodies. Ratio profiles through D-rich hot spots indicate that no significant self-diffusion of deuterium occurs between the D-rich organic matter and the depleted hydrous minerals that are surrounding them. This is not the result of a physical shielding by any constituent of the chondrites. Ab initio calculations indicate that it cannot be explained by isotopic equilibrium. Then it appears that the organic matter that is extremely enriched in D does not exchange with the hydrous minerals, or this exchange is so slow that it is not significant over the 4.5 billion year history on the parent body. If we consider that the D-rich hot spots are the result of an exposure to intense irradiation, then it appears that carbonaceous chondrites accreted organic particles that have been brought to different regions of the solar nebula. This is likely the result of important radial and vertical transport in the early solar system.

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Section: Ab Initio Modelingmentioning

confidence: 99%

Accretion and Preservation of D-Rich Organic Particles in Carbonaceous Chondrites: Evidence for Important Transport in the Early Solar System Nebula

Rémusat

Guan

Wang

et al. 2010

ApJ

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“…Vibrational frequencies (from the analytic Hessian) were calculated to ensure that each minimum is a true local minimum (containing only positive frequencies) and that each transition state has only a single imaginary frequency (negative eigenvalue of the Hessian). All QM calculations were carried out with JAGUAR (10)(11)(12). Some of these energetics were included in ref.…”

Section: Computational Detailsmentioning

confidence: 99%

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

Muller

Goddard

2002

Proc. Natl. Acad. Sci. U.S.A.

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105

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Abs efficiently catalyze the conversion of molecular singlet oxygen ( 1 O2) 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) H2O catalyzes the reaction of 1 O2 with a second water to form HOOOH; (ii) two HOOOH form a dimer, which rearranges to form the HOO-HOOO ؉ H2O complex; (iii) HOO-HOOO rearranges to HOOH-OOO, which subsequently reacts with H2O to form H2O4 ؉ HOOH; and (iv) H2O4 rearranges to the cyclic dimer (HO2)2, which in turn forms HOOH plus 1 O2 or 3 O2. Pathway II differs in that step ii is replaced with the reaction between HOOOH and 1 O2, leading to the formation of HOO-HOOO. This then proceeds to similar products. For a system with 18 The results lead to plausible mechanisms in good agreement with the Scripps isotope experiments. The Discussion talks about these results, suggesting that these mechanisms account for the Scripps Ab results and they may also be significant for understanding related processes in biochemistry, combustion, explosions, atmospheric chemistry, and radiation chemistry of aqueous systems. Computational DetailsAll QM calculations use the Becke three-parameter hybrid functional with Lee-Yang-Parr correlation functional (B3LYP) flavor of density functional theory (3-7), which includes a generalized gradient approximation and some exact exchange. The 6-31G** basis set (8, 9) was used on all atoms for a full geometry optimization. Vibrational frequencies (from the analytic Hessian) were calculated to ensure that each minimum is a true local minimum (containing only positive frequencies) and that each transition state has only a single imaginary frequency (negative eigenvalue of the Hessian). All QM calculations were carried out with JAGUAR (10-12). Some of these energetics were included in ref. 2.To obtain more accurate energetics, we carried out calculations with the cc-pVTZ basis set (13) by using the optimized geometries from the 6-31G** basis. Such QM calculations lead to an accuracy of around 3 kcal͞mol for simple organic molecules (14).For molecules such as 1 O 2 and O 3 , which have significant open shell character, standard density functional theory methods often lead to much larger errors. Thus, with B3LYP, the singlet and triplet gap for O 2 is ⌬E ( 1 ⌬ g Ϫ 3 ⌺ g Ϫ ) ϭ 10.4 kcal͞mol, in poor agreement with the experimental value of 22.5 kcal͞mol (15). Consequently, we used spin projection techniques (16) to ensure a proper description of the complexes involving 1 O 2 . This leads to ⌬E ( 1 ⌬ g Ϫ 3 ⌺ g Ϫ ) ϭ 20.5 kcal͞mol, in good agreement with experiment.The calculated vibrational frequencies (with no empirical scaling) were used to calculate the zero point energy and temperature corrections so that all energetics are reported for ⌬H (298K), in kcal͞mol. QM Calculations and Plausible MechanismsFormation of H2O2 from the Reaction Between Two H2O3. First, we examined...

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“…The dissociation constant (pKa) in aqueous solutions is calculated from a thermodynamic cycle as indicated in All gas-phase quantum mechanism calculations were carried out with the B3LYP version of the density functional theory (DFT) as implemented in the Jaguar v4.0 program [32], This includes the generalized gradient approximation (Becke non-local gradient correction), exact exchange using the Becke three-parameter exchange functional [33], and the non-local correction functional of Lee, Yang, and Parr [34]. The initial geometry of neutral AH and anion A-species were fully optimized at the B3LYP/6-31G* level.…”

Section: Theoretical Calculation Of the Acidity (Pka) Of An Acidic Comentioning

confidence: 99%

Improved Processes to Remove Naphthenic Acids

Zhang¹,

Ma²,

Wang³

et al. 2005

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In the past three years, we followed the work plan as we suggested in the proposal and made every efforts to fulfill the project objectives. Based on our large amount of creative and productive work, including both of experimental and theoretic aspects, we received important technical breakthrough on naphthenic acid removal process and obtained deep insight on catalytic decarboxylation chemistry. In detail, we established an integrated methodology to serve for all of the experimental and theoretical work. Our experimental investigation results in discovery of four type effective catalysts to the reaction of decarboxylation of model carboxylic acid compounds. The adsorption experiment revealed the effectiveness of several solid materials to naphthenic acid adsorption and acidity reduction of crude oil, which can be either natural minerals or synthesized materials. The test with crude oil also received promising results, which can be potentially developed into a practical process for oil industry. The theoretical work predicted several possible catalytic decarboxylation mechanisms that would govern the decarboxylation pathways depending on the type of catalysts being used. The calculation for reaction activation energy was in good agreement with our experimental measurements.3

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New pseudospectral algorithms for electronic structure calculations: Length scale separation and analytical two-electron integral corrections

Cited by 135 publications

References 28 publications

Accretion and Preservation of D-Rich Organic Particles in Carbonaceous Chondrites: Evidence for Important Transport in the Early Solar System Nebula

Accretion and Preservation of D-Rich Organic Particles in Carbonaceous Chondrites: Evidence for Important Transport in the Early Solar System Nebula

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

Improved Processes to Remove Naphthenic Acids

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