Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons

Lii, Jenn Huei; Allinger, Norman L.

doi:10.1021/ja00205a003

Cited by 779 publications

(417 citation statements)

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“…Our approach for the determination of the interlayer cohesive energy-using the activation energies for desorption of small polyaromatic molecules, i.e., small ''flakes of graphene''-is based on the near-additivity of such vdW interactions. 29,30 The latter is well established, for example, for the cohesive energy of alkanes where deviations from linearity in the number of chain segments are about 1% or less. 29 The activation energy for desorption-as measured by TD spectroscopy-will here be identified with the binding energy of the adsorbate to the graphite surface.…”

Section: The Interlayer Cohesive Energy Of Graphitementioning

confidence: 89%

Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons

2004

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We have studied the interaction of polyaromatic hydrocarbons ͑PAHs͒ with the basal plane of graphite using thermal desorption spectroscopy. Desorption kinetics of benzene, naphthalene, coronene, and ovalene at submonolayer coverages yield activation energies of 0.50 eV, 0.85 eV, 1.40 eV, and 2.1 eV, respectively. Benzene and naphthalene follow simple first order desorption kinetics while coronene and ovalene exhibit fractional order kinetics owing to the stability of two-dimensional adsorbate islands up to the desorption temperature. Preexponential frequency factors are found to be in the range 10 14 -10 21 s Ϫ1 as obtained from both FalconerMadix ͑isothermal desorption͒ analysis and Antoine's fit to vapor pressure data. The resulting binding energy per carbon atom of the PAH is 52Ϯ5 meV and can be identified with the interlayer cohesive energy of graphite. The resulting cleavage energy of graphite is 61Ϯ5 meV/atom, which is considerably larger than previously reported experimental values.

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Section: The Interlayer Cohesive Energy Of Graphitementioning

confidence: 89%

Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons

2004

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“…This result suggests the existence of an energy contribution that has not yet been accounted for in any of the current generation of protein potential functions. '-7 For small nonpolar organic molecules, the best current molecular mechanics force fields allow calculation of structure and energetics to within experimental a~curacy.~, 34,35 For protein molecules, which contain both polar functional groups and adjacent torsion angle degrees of freedom, the accuracy of existing molecular mechanics force fields relative to that needed to enable structure prediction is not easily evaluated. The problem of obtaining a molecular mechanics-based method for predicting protein structure can be divided into two primary subproblems: the multiple-minima problem, and the problem of obtaining an accurate representation of the energy surface of a protein and its solvent environment.…”

Section: Introductionmentioning

confidence: 99%

Accurate modeling of the intramolecular electrostatic energy of proteins

1995

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The (4, +) energy surface of blocked alanine (N-acetyl-N'-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters-in the form of partial charges, atomic multipoles, or generalized atomic densities-were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) *~uthor to whom all correspondence should be addressed. Journal of Computational

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“…The computational conformational analysis of the two diastereoisomers of 5 was carried out utilizing the MM3 force field. [6][7][8][9] An effective dielectric constant 2.0 was used in the estimation of the electrostatic interactions. Starting geometries for the MM3 search of low-energy conformations were generated by combining the anticlinal and the antiperiplanar conformations for the rotations about the O-O-bond with the different combinations of values for the dihedral angles (120.0° step) related to the rotational isomerism about the two 5-C-OO bonds.…”

Section: Methodsmentioning

confidence: 99%

Autoxidation of a 4-iminoimidazolidin-2-one with a tertiary 5-hydrogen to its 5-hydroxy derivative

Angelova¹,

Vassilev²,

Chauvin³

et al. 2008

Arkivoc

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Chemoselective autoxidation of 4-imino-1,5-dimethyl-3-(4-nitrophenyl)imidazolidin-2-one (1b) to its 5-hydroxy derivative 2 occurred in solutions of DMSO-d 6 , acetonitrile-d 3 or refluxing ethanol. Also bis(imidazolidin-5-yl) peroxide 5 was isolated as a minor product. It crystallizes as a 1:1 mixture of R*, R* and R*, S* diastereomers, whereas the NMR spectra of the reaction solution in DMSO-d 6 showed unequal amounts of the two isomers. Molecular mechanics modeling studies with the MM3 force field indicate the R*,S* diastereomer as the more stable one. The 5-unsubstituted and the 5,5-dimethyl substituted imines 1a and 1c, respectively, were found stable against autoxidation; the difference in reactivity of 1b is attributed to the single 5-methyl group enhancing the population of the enamine tautomer. The 5-hydroxy-4-imino-1,5-dimethylimidazolidin-2-one (2) underwent acid hydrolysis to form 5-hydroxyhydantoin 4.

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Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons

Cited by 779 publications

References 0 publications

Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons

Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons

Accurate modeling of the intramolecular electrostatic energy of proteins

Autoxidation of a 4-iminoimidazolidin-2-one with a tertiary 5-hydrogen to its 5-hydroxy derivative

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