Molecular mechanics. The MM3 force field for hydrocarbons. 1

Allinger, Norman L.; Yuh, Y.; Lii, Jenn Huei

doi:10.1021/ja00205a001

Cited by 2,900 publications

(1,852 citation statements)

References 3 publications

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“…We chose to use the non-reactive semi-empirical MM3 potential to model all the SAM-SAM and P2TP-SAM interactions. The MM3 potential has been shown, by us and others [5][6][7][8], to describe, quite accurately, hydrocarbons [5], fluorinated hydrocarbons [7] and multiply ringed molecules of the type we studied here. MM3 incorporates stretching, bending, and torsional energies, as well as the van der Waals S12 interaction energies based on phenomenologically determined parameters.…”

Section: Intermolecular Potential Modelsmentioning

confidence: 68%

Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

et al. 2013

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Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5′bis(4-alkylphenyl)-2,2′-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd–even effect in the strength of the intermolecular electronic coupling.

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Section: Intermolecular Potential Modelsmentioning

confidence: 68%

Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

et al. 2013

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“…58 A similar scheme has been used successfully by the MM3 force field. 50 Electrostatics. The permanent multipole moments on each atom were computed via distributed multipole analysis (DMA) 59 at the MP2/aug-cc-pVTZ level and the experimental geometry of the gas-phase monomer.…”

Section: U Ijmentioning

confidence: 99%

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Ren¹,

2003

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A new classical empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to each atomic center based on a distributed multipole analysis (DMA) derived from large basis set molecular orbital calculations on the water monomer. Polarization is treated via self-consistent induced atomic dipoles. A modified version of Thole's interaction model is used to damp induction at short range. Repulsion-dispersion (vdW) effects are computed from a buffered 14-7 potential. In a departure from most current water potentials, we find that significant vdW parameters are necessary on hydrogen as well as oxygen. The new potential is fully flexible and has been tested versus a variety of experimental data and quantum calculations for small clusters, liquid water, and ice. Overall, excellent agreement with experimental and high level ab initio results is obtained for numerous properties, including cluster structures and energetics and bulk thermodynamic and structural measures. The parametrization scheme described here is easily extended to other molecular systems, and the resulting water potential should provide a useful explicit solvent model for organic solutes and biopolymer modeling. IntroductionEmpirical potential energy functions derived from classical molecular mechanics are central to computational modeling at the atomic level. Molecular mechanics has long enjoyed great success in application to many classes of isolated, gas-phase organic compounds. 1 Beginning with the pioneering work of Bernal and Fowler, 2 water has probably been the target of more potential energy models than any other substance. An interesting overview and historical perspective on the development of water models was recently presented by Finney. 3 Simple nonpolarizable pairwise-additive models that describe the average structure and energetics of liquid water have been in wide use for many years (e.g., TIP3P 4 and SPC 5 ). The recently developed TIP5P potential exhibits excellent agreement with the experimental internal energy, density, and O‚‚‚O radial distribution at room temperature. 6 These models typically use fixed atom-based partial charges to model electrostatics and include polarization response to the environment only in an averaged, mean-field sense. As a result, nonpolarizable potentials that provide excellent descriptions of the homogeneous bulk phase are poor models for gas phase clusters and for nonpolar solutes in polar solvents. For example, the gas phase binding energy of the water dimer is overestimated by more than 30% in the TIP5P model. In application to large biomolecular systems, there is concern that such models cannot correctly account for situations where the same nonpolarizable moiety is exposed to different electrostatic environments, either within a single large static structure or during a course of simulation. In addition, there is an inherent inconsistency in most nonpolarizable models related to thei...

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“…21 In particular the MM3 22 force field has been used to run molecular dynamics at a temperature of 800 K with constrain to overcome dissociation (cumulative time of 0.1 ns, dump time 1 ps). 100 snapshots are then optimized with a convergence of 10 À6 kcal mol À1 Å À1 RMS gradient per atom.…”

Section: Theoretical Sectionmentioning

confidence: 99%

Chiral recognition between 1-(4-fluorophenyl)ethanol and 2-butanol: higher binding energy of homochiral complexes in the gas phase

Rondino

Paladini

Ciavardini

et al. 2011

Phys. Chem. Chem. Phys.

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Diastereomeric adducts between (S)-1-(4-fluorophenyl)-ethanol and R and S 2-butanol, formed by supersonic expansion, have been investigated by means of a combination of mass selected resonant two-photon ionization-spectroscopy and infrared depletion spectroscopy. Chiral recognition is evidenced by the specific spectroscopic signatures of the S 1 ' S 0 electronic transition as well as different frequencies and intensities of the OH stretch vibrational mode in the ground state. D-DFT calculations have been performed to assist in the analysis of the spectra and the determination of the structures. The homochiral and heterochiral complexes show slight structural differences, in particular in the interaction of the alkyl groups of 2-butanol with the aromatic ring. The experimental results show that the homochiral [FE S ÁB S ] complex is more stable than the heterochiral [FE S ÁB R ] diastereomer in both the ground and excited states. The binding energy difference has been evaluated to be greater than 0.60 kcal mol À1 .

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Molecular mechanics. The MM3 force field for hydrocarbons. 1

Cited by 2,900 publications

References 3 publications

Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Chiral recognition between 1-(4-fluorophenyl)ethanol and 2-butanol: higher binding energy of homochiral complexes in the gas phase

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