General atomic and molecular electronic structure system

Schmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A.; Elbert, Stephen T.; Gordon, Mark S.; Jensen, Jan H.; Koseki, Shiro; Matsunaga, Nikita; Nguyen, Kiet A.; Su, Shujun; Windus, Theresa L.; Dupuis, Michel; Montgomery, John A.

doi:10.1002/jcc.540141112

Cited by 19,848 publications

(12,457 citation statements)

References 115 publications

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“…Table 1 compares properties of the five potential surfaces used in the dynamics calculations. Also presented are results from AM1, PM3 (for which we use GAMESS 49 ), and high level ab initio calculations. 50,51 Despite the greatly overestimated reaction barrier, MSINDO predicts a transition state (TS) geometry and reaction energy noticeably closer to ab initio results than does AM1 or PM3.…”

Section: Resultsmentioning

confidence: 99%

H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

Camden

Bechtel

et al. 2005

J. Phys. Chem. A

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We compare experimental photoloc measurements and quasi-classical trajectory calculations of the integral cross sections, lab-frame speed distributions, and angular distributions associated with the CD 3 products of the H + CD 4 (ν ) 0) f CD 3 + HD reaction at collision energies ranging from 0.5 to 3.0 eV. Of the potential energy surfaces (PES) we explored, the direct dynamics calculations using the B3LYP/6-31G** density functional theory PES provide the best agreement with the experimental measurements. This agreement is likely due to the better overall description that B3LYP provides for geometries well removed from the minimum energy path, even though its barrier height is low by ∼0.2 eV. In contrast to previous theoretical calculations, the angular distributions on this surface show behavior associated with a stripping mechanism, even at collision energies only ∼0.1 eV above the reaction barrier. Other potential energy surfaces, which include an analytical potential energy surface from Espinosa-García and a direct dynamics calculation based on the MSINDO semiempirical Hamiltonian, are less accurate and predict more rebound dynamics at these energies than is observed. Reparametrization of the MSINDO surface, though yielding better agreement with the experiment, is not sufficient to capture the observed dynamics. The differences between these surfaces are interpreted using an analysis of the opacity functions, where we find that the wider cone of acceptance on the B3LYP surface plays a crucial role in determining the integral cross sections and angular distributions.

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Section: Resultsmentioning

confidence: 99%

H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

Camden

Bechtel

et al. 2005

J. Phys. Chem. A

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“…Because NBD-diC 16 PE is anionic at pH close to neutrality, 42 the probes were modelled with global charge À1, with a single hydrogen atom bound to the amine nitrogen. Partial charges of a NBD-diC 3 PE molecule were derived from ab initio quantum mechanical calculations 43 using Gamess-US, 44,45 and used for all studied derivatives. Fig.…”

Section: Simulation Detailsmentioning

confidence: 99%

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

Filipe

Santos

Ramalho

et al. 2015

Phys. Chem. Chem. Phys.

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A complete homologous series of fluorescent phosphatidylethanolamines (diC n PE), labelled at the head group with a 7-nitrobenz-2-oxa-1,3-diazo-4-yl(NBD) fluorophore and inserted in 1-palmitoyl, 2-oleoyl-snglycero-3-phosphocholine (POPC) bilayers, was studied using atomistic molecular dynamics simulations. The longer-chained derivatives of NBD-diC n PE, with n = 14, 16, and 18, are commercially available, and widely used as fluorescent membrane probes. Properties such as location of atomic groups and acyl chain order parameters of both POPC and NBD-diC n PE, fluorophore orientation and hydrogen bonding, membrane electrostatic potential and lateral diffusion were calculated for all derivatives in the series. Most of these probes induce local disordering of POPC acyl chains, which is on the whole counterbalanced by ordering resulting from binding of sodium ions to lipid carbonyl/glycerol oxygen atoms. An exception is found for NBD-diC 16 PE, which displays optimal matching with POPC acyl chain length and induces a slight local ordering of phospholipid acyl chains. Compared to previously studied fatty amines, acyl chain-labelled phosphatidylcholines, and sterols bearing the same fluorescent tag, the chromophore in NBD-diC n PE locates in a similar region of the membrane (near the glycerol backbone/carbonyl region) but adopts a different orientation (with the NO 2 group facing the interior of the bilayer). This modification leads to an inverted orientation of the P-N axis in the labelled lipid, which affects the interface properties, such as the membrane electrostatic potential and hydrogen bonding to lipid head group atoms. The implications of this study for the interpretation of the photophysical properties of NBD-diC n PE (complex fluorescence emission kinetics, differences with other NBD lipid probes) are discussed.

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“…Thedispersion correction was taken into account using the DFT-D3 program package by Grimme et al [44]. The effect of the aqueous environment was simulated within the supermolecular approximation and within the continuous solvent model (CPCM), using the US GAMESS program package [45]. (Fig.…”

Section: Quantum-chemical Calculationsmentioning

confidence: 99%

Catalytic performance of carbon nanotubes in H2O2 decomposition: Experimental and quantum chemical study

Voitko

Toth

Demianenko

et al. 2015

Journal of Colloid and Interface Science

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The catalytic performance of multi-walled carbon nanotubes (MWCNTs) with different surface chemistry was studied in the decomposition reaction of H 2 O 2 at various values of pH and temperature. A comparative analysis of experimental and quantum chemical calculation results is given. It has been shown that both the lowest calculated activation energy (~18.9 kJ/mol) and the highest rate cons tant correspond to the N-containing CNT. The calculated chemisorption energy values correlate with the operation stability of MWCNTs. Based on the proposed quantum chemical model it was found that the catalytic activity of carbon materials in electron tran sfer reactions is controlled by their electron donor capability.

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General atomic and molecular electronic structure system

Cited by 19,848 publications

References 115 publications

H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

Catalytic performance of carbon nanotubes in H2O2 decomposition: Experimental and quantum chemical study

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General atomic and molecular electronic structure system

Cited by 19,848 publications

References 115 publications

H + CD4 Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

H + CD4 Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

Catalytic performance of carbon nanotubes in H2O2 decomposition: Experimental and quantum chemical study

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H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

H + CD₄ Abstraction Reaction Dynamics: Excitation Function and Angular Distributions