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Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation
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10.1063/1.3476466
/content/aip/journal/jcp/133/9/10.1063/1.3476466
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/9/10.1063/1.3476466

Figures

Image of FIG. 1.
FIG. 1.

Numbering scheme for aldopyranoses rings.

Image of FIG. 2.
FIG. 2.

Schematic representation of stable ring conformers, located on the plane of Cremer–Pople coordinates: chair (a); inverted chair (b) boats [(c) and (e)]; skew-boats [(e) and (f)]. Exact chair conformers have been represented out of the diagram, to underline that for them the angle is not defined.

Image of FIG. 3.
FIG. 3.

Puckering free energy landscape (already corrected with the results from the umbrella sampling phase) of -D-Glc using the standard 45a4 parameter set. Upper panel: the plane is shown, with isolines drawn every 10 kJ/mol starting from the absolute minimum. Lower panel: projection of the free energy profile onto the plane. Darker colors correspond to lower energies.

Image of FIG. 4.
FIG. 4.

Contribution to the total puckering free energy of -D-Glc (45a4 parameters) from the equilibrium sampling, . An immaterial constant has been added so that the correction term is zero at the position of the free energy global minimum. Isolines are drawn every 2.5 kJ/mol (upper panel). The projection onto the plane of the correction term (lower panel).

Image of FIG. 5.
FIG. 5.

Inverted chair free energy difference for the (upper panel) and (lower panel) series of aldopyranoses. The three curves refer to the simulation results obtained using the 45a4 parameter set (squares) and the predictions in Ref. 61 (triangles) and Ref. 62 (circles). Diamonds correspond to the estimates from NMR measurements (idose, Ref. 50; altrose, this work). Lines are a guide to the eye, and error bars are always smaller than the symbols (0.5 kJ/mol).

Image of FIG. 6.
FIG. 6.

Results of the unbiased molecular dynamics simulation of -D-Glc. Histogram of the population along the puckering coordinate (upper panel) and time evolution of the number of inverted chairs (lower panel).

Image of FIG. 7.
FIG. 7.

Inverted chair free energy difference for the (upper panel) and (lower panel) series of aldopyranoses. The three curves refer to the simulation results using the new parameter set (squares) and the predictions in Ref. 61(triangles) and Ref. 62 (circles). Diamonds correspond to the estimates from NMR measurements (idose, Ref. 50; altrose, this work). Lines are a guide to the eye and error bars are always smaller than the symbols (0.5 kJ/mol).

Image of FIG. 8.
FIG. 8.

Puckering free energy landscapes (in kJ/mol) obtained by the combined metadynamics-umbrella sampling, for the series of -D-aldopyranoses simulated using the new force field parameters. Isolines are drawn every 10 kJ/mol, starting from the global minimum.

Image of FIG. 9.
FIG. 9.

Puckering free energy landscapes (in kJ/mol) obtained by the combined metadynamics-umbrella sampling, for the series of -D-aldopyranoses simulated using the new force field parameters. Isolines are drawn every 10 kJ/mol, starting from the global minimum.

Tables

Generic image for table
Table I.

Orientation of ring substituents (ax: axial; eq: equatorial) for different stereoisomers (referred to the conformer).

Generic image for table
Table II.

Assigned chemical shifts and coupling constants for the four main forms of altropyranose. [Chemical shifts of and are reported in ppm; coupling constants are reported in Hz.]

Generic image for table
Table III.

Free energy and population of different conformers using the 45a4 parameter set (energies are expressed in kJ/mol, angles are in rad, and probabilities in percent).

Generic image for table
Table IV.

New parameters for D-aldopyranoses torsional interactions.

Generic image for table
Table V.

Free energy and population of different conformers using the new parameter set (energies are expressed in kJ/mol, angles are in rad, and probabilities in percent).

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/content/aip/journal/jcp/133/9/10.1063/1.3476466
2010-09-07
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/9/10.1063/1.3476466
10.1063/1.3476466
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