Anomeric free energy of D-mannose in water: A comparison of free energy perturbation, potential of mean force, and MC(JBW)/SD simulations

Hanoch Senderowitz; W. Clark Still

doi:10.1021/jp962437s

Anomeric free energy of D-mannose in water: A comparison of free energy perturbation, potential of mean force, and MC(JBW)/SD simulations

Hanoch Senderowitz, W. Clark Still

Columbia University

Research output: Contribution to journal › Review article › peer-review

10 Scopus citations

Abstract

The anomeric free energy difference between the α (axial) and β (equatorial) anomers of D-mannose was calculated using standard free energy methods (free energy perturbation (FEP) and potential of mean force (PMF)) and with the recently described MC(JBW)/SD simulation technique. The final results obtained with our new united atom AMBER* force field and GB/SA continuum water are FEP 0.28 ± 0.10, PMF 0.20 ± 0.10, MC(JBW)/SD, and 0.25 ± 0.02 kcal/mol in favor of the α anomer, all in good agreement with the experimental value (0.34-0.45 kcal/mol). Convergence, as measured by the stability of the results and the standard deviations, is reached at least an order of magnitude faster with MC(JBW)/SD than with the other two methods.

Original language	English
Pages (from-to)	1409-1412
Number of pages	4
Journal	Journal of Physical Chemistry B
Volume	101
Issue number	8
DOIs	https://doi.org/10.1021/jp962437s
State	Published - 20 Feb 1997
Externally published	Yes

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abstract = "The anomeric free energy difference between the α (axial) and β (equatorial) anomers of D-mannose was calculated using standard free energy methods (free energy perturbation (FEP) and potential of mean force (PMF)) and with the recently described MC(JBW)/SD simulation technique. The final results obtained with our new united atom AMBER* force field and GB/SA continuum water are FEP 0.28 ± 0.10, PMF 0.20 ± 0.10, MC(JBW)/SD, and 0.25 ± 0.02 kcal/mol in favor of the α anomer, all in good agreement with the experimental value (0.34-0.45 kcal/mol). Convergence, as measured by the stability of the results and the standard deviations, is reached at least an order of magnitude faster with MC(JBW)/SD than with the other two methods.",

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AU - Still, W. Clark

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AB - The anomeric free energy difference between the α (axial) and β (equatorial) anomers of D-mannose was calculated using standard free energy methods (free energy perturbation (FEP) and potential of mean force (PMF)) and with the recently described MC(JBW)/SD simulation technique. The final results obtained with our new united atom AMBER* force field and GB/SA continuum water are FEP 0.28 ± 0.10, PMF 0.20 ± 0.10, MC(JBW)/SD, and 0.25 ± 0.02 kcal/mol in favor of the α anomer, all in good agreement with the experimental value (0.34-0.45 kcal/mol). Convergence, as measured by the stability of the results and the standard deviations, is reached at least an order of magnitude faster with MC(JBW)/SD than with the other two methods.

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Anomeric free energy of D-mannose in water: A comparison of free energy perturbation, potential of mean force, and MC(JBW)/SD simulations

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