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M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures

Molinero, Valeria and Goddard, William A., III (2004) M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures. Journal of Physical Chemistry B, 108 (4). pp. 1414-1427. ISSN 1520-6106. doi:10.1021/jp0354752. https://resolver.caltech.edu/CaltechAUTHORS:20170705-092528499

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Abstract

We derive a chemically realistic coarse grain model and force field for the simulation of malto-oligosaccharides (α(1→4) d-glucans) and their aqueous mixtures. This coarse grain model for carbohydrates (denoted M3B) represents each glucose monomer by three beads while describing the water molecule as a single particle. M3B includes no charges or hydrogen-bonding terms, using only two-body Morse functions to describe long-range forces. The configurations obtained with the M3B model map uniquely and quickly back to a full atomistic description. M3B was parametrized to fit the results from atomistic simulations for the gas phase and amorphous bulk phase of sugars over a wide range of pressures. In particular, we required that the M3B force field provide an accurate representation of such quantities as excluded volume interactions and the distribution of torsional configurations about the intermonomer bonds. We find that M3B leads to a helical structure for polysaccharide chains and predicts left-handed helices to be more stable than right-handed ones, in agreement with the experiments. We find that parallel and antiparallel double-helical bulk structures of malto-oligosaccharides are feasible and of similar energy. The M3B model leads to a glass transition temperature (T_g) for glucose of 296 K in good agreement with experiment (304 K) and a T_g for 12 wt % water−glucose mixtures of 239 K in good agreement with experiment (240 K). These results suggest that these characteristic physical properties of carbohydrates can be described well without the use of explicit hydrogen bonds or electrostatics and also without introducing explicit directional forces in the nonbonded interactions. Molecular dynamics (MD) simulations with M3B are ∼7000 times faster than fully flexible atomistic simulations, making it practical to study large systems for long times. We expect that M3B will be of use for the study of the structure and dynamics of complex syrups and supercooled carbohydrates solutions.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/jp0354752DOIArticle
http://pubs.acs.org/doi/abs/10.1021/jp0354752PublisherArticle
http://pubs.acs.org/doi/suppl/10.1021/jp0354752PublisherSupporting Information
ORCID:
AuthorORCID
Goddard, William A., III0000-0003-0097-5716
Additional Information:© 2004 American Chemical Society. Received 27 May 2003. Published online 7 January 2004. Published in print 1 January 2004. We acknowledge Tahir Cagin, Brian Guthrie, Michael Tanoff, and Gary A. Day for their comments and in particular we thank Alejandro Strachan for his enthusiastic help with the MCSA optimization procedure. We thank referee 1 for his/her spectacular effort in checking our results, finding a numerical error, and for kindly providing his/her own atomistic structures of the right- and left-handed DP12. The facilities of the Materials and Process Simulation Center are supported by ONR-DURIP, ARO-DURIP, SIR-IBM, NSF (CHE), and additional support is provided by DOE-ASCI, DOE-FETL, ARO-MURI, ONR-MURI, NIH, NSF, Kellogg's, General Motors, ChevronTexaco, Seiko-Epson, Beckman Institute and Asahi Kasei.
Funders:
Funding AgencyGrant Number
Office of Naval Research (ONR)UNSPECIFIED
Army Research Office (ARO)UNSPECIFIED
IBMUNSPECIFIED
NSFUNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
NIHUNSPECIFIED
Kellogg'sUNSPECIFIED
General MotorsUNSPECIFIED
ChevronTexacoUNSPECIFIED
Seiko-EpsonUNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Asahi KaseiUNSPECIFIED
Issue or Number:4
DOI:10.1021/jp0354752
Record Number:CaltechAUTHORS:20170705-092528499
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170705-092528499
Official Citation:M3B:  A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures Valeria Molinero and William A. Goddard III The Journal of Physical Chemistry B 2004 108 (4), 1414-1427 DOI: 10.1021/jp0354752
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:78755
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:06 Jul 2017 23:01
Last Modified:15 Nov 2021 17:42

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