Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis

Breneman, Curt M.; Wiberg, Kenneth B.

doi:10.1002/jcc.540110311

Cited by 4,468 publications

(3,498 citation statements)

References 12 publications

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“…The DFT calculations were performed with the Q-Chem quantum chemistry package 21 using the B3LYP level of theory and the 6-31G* basis set, partial atomic charges were obtained using the ChelpG technique. 22 To determine the binding energy geometry optimisations were performed at the B3LYP/6-31G** level of theory, and the binding energies were subsequently calculated at the higher B3LYP /6-311++G** level as follows BE = E(complex) -E(linker) -E opt (CH 4 ).…”

Section: Modelling and Simulationsmentioning

confidence: 99%

A Novel Bismuth‐Based Metal–Organic Framework for High Volumetric Methane and Carbon Dioxide Adsorption

Savage

Yang

Suyetin

et al. 2014

Chemistry A European J

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Section: Modelling and Simulationsmentioning

confidence: 99%

A Novel Bismuth‐Based Metal–Organic Framework for High Volumetric Methane and Carbon Dioxide Adsorption

Savage

Yang

Suyetin

et al. 2014

Chemistry A European J

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“…The more positive the carbon atom, the more it would be expected to be deshielded in the NMR spectrum, and it is interesting to note that the trends in charge are in excellent agreement with the 13 C chemical shifts for these molecules. 30 An analysis of the Mulliken charges vs. 13 C chemical shifts gave rise to an average correlation coefficient of 0.96.…”

Section: Configurational Effectsmentioning

confidence: 99%

Solvated ensemble averaging in the calculation of partial atomic charges

Basma¹,

Sundara²,

Çalgan³

et al. 2001

J Comput Chem

139

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In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvation. Carbohydrates contain numerous hydroxyl groups that exist in an ensemble of orientations in solution, and in this report we apply ensemble averaging to a series of methyl glycosides. We report the extent to which ensemble averaging leads to charge convergence among the various monosaccharides and among the constituent atoms within a given monosaccharide. Due to the large number of conformations (200) in our ensembles, we are able to compute statistically relevant standard deviations for the partial charges. An analysis of the standard deviations allows us to assess the extent to which equivalent atom types may, nevertheless, require unique partial charges. The configurations of the hydroxyl groups exert considerable influence on internal energies, and the limits of ensemble averaged charges are discussed in terms of these properties.

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“…The atom spheres were defined according to the CHELPG scheme. 21 Figure 1 depicts the optimized geometries (0 K) of isolated ions and ion pairs. The atoms are colored according to their polarity.…”

Section: Simulation Methodsologymentioning

confidence: 99%

Polarization versus Temperature in Pyridinium Ionic Liquids

Chaban

Prezhdo

2014

J. Phys. Chem. B

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Abstract. Electronic polarization and charge transfer effects play a crucial role in thermodynamic, structural and transport properties of room-temperature ionic liquids (RTILs).These non-additive interactions constitute a useful tool for tuning physical chemical behavior of RTILs. Polarization and charge transfer generally decay as temperature increases, although their presence should be expected over an entire condensed state temperature range. For the first time, we use three popular pyridinium-based RTILs to investigate temperature dependence of electronic polarization in RTILs. Atom-centered density matrix propagation molecular dynamics, supplemented by a weak coupling to an external bath, is used to simulate the temperature impact on system properties. We show that, quite surprisingly, non-additivity in the cation-anion interactions changes negligibly between 300 and 900 K, while the average dipole moment increases due to thermal fluctuations of geometries. Our results contribute to the fundamental understanding of electronic effects in the condensed phase of ionic systems and foster progress in physical chemistry and engineering.

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Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis

Cited by 4,468 publications

References 12 publications

A Novel Bismuth‐Based Metal–Organic Framework for High Volumetric Methane and Carbon Dioxide Adsorption

A Novel Bismuth‐Based Metal–Organic Framework for High Volumetric Methane and Carbon Dioxide Adsorption

Solvated ensemble averaging in the calculation of partial atomic charges

Polarization versus Temperature in Pyridinium Ionic Liquids

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