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Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups
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10.1063/1.3664300
/content/aip/journal/jcp/135/21/10.1063/1.3664300
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/21/10.1063/1.3664300

Figures

Image of FIG. 1.
FIG. 1.

The general repartitioning scheme used in QM/MM-simulations: a large system is split into two regions, a small quantum-mechanical, and a large classical box. The covalent bonds connecting the two regions must be saturated on the quantum side.

Image of FIG. 2.
FIG. 2.

The reference systems (left column) and their corresponding capped systems (right column). The capping-potential is denoted as “D”.

Image of FIG. 3.
FIG. 3.

Maximum relative errors of the bond lengths caused by the use of our capping-potentials and the more common fluorine- and hydrogen-capping as well as Komin's PSP in molecules I-V (see Figure 2). Both stretched and shortened covalent bonds are plotted separately. The bond with the capping-potential was not taken into account.

Image of FIG. 4.
FIG. 4.

Potential curves for the bond between the carbon atom and the capping-potential (after full relaxation of the remaining degrees of freedom). The zero-point of the energy scale is set to the energy of the equilibrium structure.

Image of FIG. 5.
FIG. 5.

Potential curves for the bond between the carbon atom and the nitrogen/oxygen-atom in the functional group, using a geometry-optimized structure. The zero-point of the energy scale is set to the energy of the relaxed structure. For the carboxylic acid the single-bonded oxygen atom was examined.

Image of FIG. 6.
FIG. 6.

Average absolute errors in the chemical shifts (a) hydrogen, (b) carbon, (c) oxygen, and (d) nitrogen) caused by the capping. Shown are the errors for our optimized potentials, fluorine, and hydrogen cappings, as well as a potential from previous work done by Komin and Sebastiani.46 The striped bars represent the geometry that was used for finding the capping-potential, the solid bars show the results for the re-optimized geometry.

Image of FIG. 7.
FIG. 7.

Two butanoic-acid molecules with hydrogen bonds, which we used to benchmark our capping-potentials. The translucent atoms are only included in the reference calculation. The carbon atom drawn in dark gray represents the cleavage site.

Image of FIG. 8.
FIG. 8.

Potential curve for the distance of the application setup shown in Figure 7. Shown are the reference calculation, our capping-potential and hydrogen-capping. For the calculation equilibrated geometries were used and the energy zero point is set to the minimum energy.

Tables

Generic image for table
Table I.

The pseudopotentials that are optimized for different capping situations. For comparison, Komin's PSP (Ref. 46) and the regular atomic pseudopotentials for carbon and hydrogen are listed. The meaning of the different parameters is discussed in the original publication (Ref. 34).

Generic image for table
Table II.

Wavenumber differences for intramolecular vibrations between carbon and the capping potential: .

Generic image for table
Table III.

Wavenumber differences () for intramolecular vibrations between carbon and either oxygen or nitrogen. For butanioc-acid, the single-bonded oxygen was evaluated.

Generic image for table
Table IV.

RMSE of the chemical shifts shown in Figure 6.

Generic image for table
Table V.

Properties of the hydrogen bonds computed by using our capping-potential or hydrogen capping, compared with the full quantum reference (calculated as X cap X ref ). The atomic labels are shown in Figure 7. A negative represents a more attractive hydrogen bond.

Generic image for table
Table VI.

Wavenumbers for the intermolecular mode of the butanoic-acid dimer, assuming rigid molecules.

Generic image for table
Table VII.

The deviations of the chemical shifts in the capped system caused by our capping-potential and hydrogen-capping. For the carbon and hydrogen atoms that are not listed explicitly, we have taken the average of the absolute errors.

Generic image for table
Table VIII.

The deviations in the proton affinities E pa (calculated as E pa, cap E pa, ref ) for the butanoate-ion and butylamine, computed using our capping potentials as well as hydrogen-capping. A positive ΔE pa indicates a stronger proton affinity than the reference.

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/content/aip/journal/jcp/135/21/10.1063/1.3664300
2011-12-06
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/21/10.1063/1.3664300
10.1063/1.3664300
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