On the definition of the atomic charge. Relationship between13C NMR chemical shifts, dipole moments, and charges in saturated hydrocarbons

Monaco, Guglielmo

doi:10.1002/(sici)1097-461x(1998)68:3<201::aid-qua6>3.0.co;2-z

Cited by 4 publications

(3 citation statements)

References 31 publications

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“…Reed and Weinhold have discussed the large negative charge on carbon atoms in alkanes in the NPA model. They argue that dipolar distributions caused by the hybridization used in the technique will alter properties generated by this charge, such as molecular dipoles . Presumably, such effects will also influence the interactions that we are attempting to model.…”

Section: Discussionmentioning

confidence: 99%

Through-Space Charge and Dipolar Effects in Substituted Ethanes and 1,1,1-Trifluoroethanes

Nolan

Linck

2001

J. Phys. Chem. A

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The results of ab initio calculations with the 6-31+G* basis set are reported on over sixty compounds of the type CZ 3 CH 2 X (Z ) H, F) and on a few longer chain-substituted alkanes. Data for the eclipsed conformations with Z ) H and both the staggered and eclipsed conformations with Z ) F are presented. The charges on the atoms in these molecules are determined with the Atoms in Molecules (AIM) and Natural Population Analysis (NPA) methods of analysis. The charges on the fluorine atoms in the trifluoroethyl derivatives parallel those of the hydrogen atoms of the ethyl derivatives. A potential gradient model for charge variations is presented. In this model, the magnitude of the charge is dictated by a through-space electrostatic interaction that arises from the charges on the atoms of the CH 2 X group. The length of the vectors from the atoms in the CH 2 X group to the bond critical point of the C-Z (Z ) H, F) bond and the angle this vector makes with the C-Z bond are critical parameters. The model is tested in systems in which the charge of the methylene carbon atom can be ignored, as well as more rigorously with inclusion of the charge of the methylene carbon atom. The potential gradient model accounts for a greater positive (negative) charge on the antiperiplanar atom than on the gauche ones (staggered conformer) and on the gauche compared to synperiplanar (eclipsed conformer) for positively (negatively) charged X. The model also gives a rationalization for the change in charge observed on the Z atoms when X ) EH n q is replaced by X ) EF n q . Comparisons of antiperiplanar and eclipsed conformers of CH 3 CH 2 X and CF 3 CH 2 X show that these conformational changes have little effect on the charges of the atoms in the methylene (CH 2 X) fragment.

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Section: Discussionmentioning

confidence: 99%

Through-Space Charge and Dipolar Effects in Substituted Ethanes and 1,1,1-Trifluoroethanes

Nolan

Linck

2001

J. Phys. Chem. A

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“…It is known that neighboring residues [1] have a significant effect on chemical shift, which is commonly related to atomic charge. [2,3] For example, neighboring amino acids in catalytic triads are often ignored but, surprisingly, these residues are strongly conserved in Nature and are important to the function and structure of the active site. [4] Surprisingly little effort has been made to show the effects of neighboring residues on the atomic charges used so confidently by modern force fields.…”

Section: Introductionmentioning

confidence: 99%

“…However, a given atom does experience significant charge transfer and polarization effects from the neighboring residue, neither of which is well‐handled by traditional force fields. It is known that neighboring residues have a significant effect on chemical shift, which is commonly related to atomic charge . For example, neighboring amino acids in catalytic triads are often ignored but, surprisingly, these residues are strongly conserved in Nature and are important to the function and structure of the active site .…”

Section: Introductionmentioning

confidence: 99%

Toward amino acid typing for proteins in FFLUX

Fletcher¹,

Popelier

2016

J Comput Chem

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Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic charges in a peptide chain respond to the substitution of a neighboring residue and this response can be categorized in a manner similar to atom-typing. Using a machine learning method called kriging, we are able to build predictive models for an atom that is defined, not only by its local environment, but also by its neighboring residues, for a minimal additional computational cost. We found that prediction errors were up to 11 times lower when using a model specific to the correct group of neighboring residues, with a mean prediction of $0.0015 au. This finding suggests that atoms in a force field should be defined by more than just their immediate atomic neighbors. When comparing an atom in a single alanine to an analogous atom in a deca-alanine helix, the mean difference in charge is 0.026 au. Meanwhile, the same difference between a trialanine and a deca-alanine helix is only 0.012 au. When compared to deca-alanine models, the transferable models are up to 20 times faster to train, and require significantly less ab initio calculation, providing a practical route to modeling large biological systems.

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On the charge distribution in ethanes and disilanes and correlations with equilibrium bond lengths; an ab initio study

Palmer

2000

Journal of Molecular Structure: THEOCHEM

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On the definition of the atomic charge. Relationship between13C NMR chemical shifts, dipole moments, and charges in saturated hydrocarbons

Cited by 4 publications

References 31 publications

Through-Space Charge and Dipolar Effects in Substituted Ethanes and 1,1,1-Trifluoroethanes

Through-Space Charge and Dipolar Effects in Substituted Ethanes and 1,1,1-Trifluoroethanes

Toward amino acid typing for proteins in FFLUX

On the charge distribution in ethanes and disilanes and correlations with equilibrium bond lengths; an ab initio study

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