Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations

Naidoo, Kevin J.; Kuttel, Michelle M.

doi:10.1002/1096-987x(200103)22:4<445::aid-jcc1015>3.0.co;2-p

Cited by 69 publications

(81 citation statements)

References 54 publications

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“…195,277,[296][297][298]300,301,306 These were obtained by placing the solute in its initial configuration at the center of a cube of edge length 1.5 nm spanned by a threedimensional cubic grid with 100 grid points along each dimension. Successive configurations along the trajectory were superimposed onto this initial configuration by means of a roto-translational least-squares fit 322 based on the sugar heavy atoms (excluding O 6 ).…”

Section: Discussionmentioning

confidence: 99%

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

Kräutler

Müller

Hünenberger

2007

Carbohydrate Research

139

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Section: Discussionmentioning

confidence: 99%

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

Kräutler

Müller

Hünenberger

2007

Carbohydrate Research

139

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“…For the Wigner-Seitz cell of hexagonal ice, the nonsphericity is estimated as 2.25 [15], whereas it is equal to 3.31 for ideal tetrahedron. Unlike fullerenes, water clusters having the shape of convex polyhedra with the predominant number of pentagonal faces can be less stable than the aggregates of other shapes [6].…”

Section: The Modified Methods Of Statistical Geometrymentioning

confidence: 99%

Computer Simulation of the Absorption of CO2 Molecules by Water Cluster: 2. The Microstructure

2005

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The simulation of the absorption of CO 2 molecules by the (H 2 O) 10 cluster is performed by the molecular dynamics method using the modified TIP4P model of water. The detailed structure of (CO 2 ) i (H 2 O) 10 clusters ( 0 ≤ i ≤ 11 ) is analyzed by the statistic geometry method based on the construction of the Voronoi polyhedra. The obtained distributions of the geometric elements of polyhedra indicate the significant changes in the structure of a cluster after the absorption of one CO 2 molecule. Only polyhedra characterizing the structure of unstable water clusters that absorbed six or seven CO 2 molecules demonstrate a nonsphericity close to the ideal tetrahedron. Linear CO 2 molecule tends to be oriented in a cluster so that the average angle formed by this molecule and permanent dipole moments of water molecules would be equal to about 30 ° .

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“…Palma et al [118] later corrected the O-C-C-O term to revise the barrier of hydroxyl rotations (PHLB model). Kuttel, Brady, and Naidoo modified the PHLB parameter set for lower primary alcohol rotational barriers and referred to the force field as the Carbohydrate Solution Force Field (CSFF) [119][120]. Recently, MacKerell et al [116] have developed atomistic force fields for carbohydrates building upon the CHARMM force field platform.…”

Section: Charge Equilibration Carbohydrate Force Fieldsmentioning

confidence: 99%

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

Bauer

Patel

2012

Theor Chem Acc

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With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, in our hands those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for small molecules, proteins, lipids, and lipid bilayers and recently have begun work on carbohydrate force fields. The latter area has been relatively untouched by force field developers with particular focus on polarizable, non-additive interaction potential models. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration method for phasedependent polarizable force fields, lipid molecules, and small-molecule carbohydrates. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields.

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Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations

Cited by 69 publications

References 54 publications

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

Computer Simulation of the Absorption of CO2 Molecules by Water Cluster: 2. The Microstructure

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

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