Correlated <i>ab initio</i> quantum chemical calculations of di‐ and trisaccharide conformations

Gould, Ian R.; Bettley, Hoda Abdel Aal; Bryce, Richard A.

doi:10.1002/jcc.20738

Cited by 9 publications

(11 citation statements)

References 51 publications

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“…In the former system, instead, two areas are sampled, around (-25°; -20°) and (-65°; -50°), for 70 % and 30 % of the total simulation time, respectively. It is difficult to validate these results, as no experimental data exist in the literature for P( Φ H , Ψ H ) of C 12 G 2 micelles and these results differ for a maltose molecule in water where experimental (such as NMR32,38,108,109 or optical rotation 110) and theoretical studies (such as QM38,111,112 and MD 28,32,37,69,113) predicted two peaks for P( Φ H , Ψ H ) around (-50°; -30°) ± 20° and (-40°; -30°) ± 20°.…”

Section: Resultsmentioning

confidence: 97%

Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

et al. 2010

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This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-Dodecyl-ß-maltoside (C 12 G 2 ), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure and hydration of the C 12 G 2 anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M. et al. J. Comp. Chem. 2002, 23, 1236-1243. We find that our CHARMM and GLYCAM parameter sets yields similar results in case of properties related to the micelle structure, but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C 12 G 2 micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 Å and 25.4 Å for the α-and β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7 -11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in α-or β-anomers.

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Section: Resultsmentioning

confidence: 97%

Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

et al. 2010

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“…To date, the following theoretical models and methods are applied for in silico design of carbohydrate three-dimensional structure [ 112 , 113 , 114 , 115 , 116 ]: Molecular mechanics (MM) and molecular dynamics (MD) calculations [ 117 ]; Monte Carlo simulations [ 118 , 119 ]; Semi-empirical methods [ 120 , 121 , 122 , 123 ]; Ab initio simulations based on density functional theory (DFT) [ 124 , 125 , 126 , 127 , 128 ]; Hybrid QM/MM and QM/QM and ONIOM (“our own N-layered integrated molecular orbital and molecular mechanics”) approaches [ 129 , 130 , 131 , 132 , 133 , 134 ]. …”

Section: Carbohydrate 3d Structure Modelingmentioning

confidence: 99%

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Scherbinina

Toukach

2020

IJMS

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Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

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“…During these 2 last decades, many works dealing with conformational studies of carbohydrates have appeared; most of them used classical methods to explore the structure of the conformers, such as molecular mechanics 2–15. More recently, a number of articles, using ab initio or density functional theory (DFT) studies, have begun to appear 15–23…”

Section: Introductionmentioning

confidence: 99%

“…DFT and, in general, ab initio methods are not so simple to use when dealing with compounds that have a variety of conformers, such as carbohydrates, as, calculation of the conformational space or the energy hypersurface of mono, di, or trisaccharides by such methods requires enormous CPU time 22–25…”

Section: Introductionmentioning

confidence: 99%

“…On the other hand, the MP2/6‐31G(d) method has also been used to obtain energies and structures of these conformers, first by relaxing all the degrees of freedom of the molecule except the two dihedral angles that have been kept frozen and then by performing full optimizations. We have compared the effect of these correlated methods as they have been proved to yield more reliable results and to be less susceptible to intramolecular BSSE, this feature is important and must be taken into account especially in the case of some folded conformers of oligosaccharides 22, 28…”

Section: Introductionmentioning

confidence: 99%

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Relaxed energetic maps of κ‐carrabiose: A DFT study

et al. 2010

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The B3LYP density function was used with the 6-31G(d) basis set to perform relaxed energetic contour maps of the charged form of kappa-carrabiose in the gas phase and for the neutral form first in the gas phase and then by simulating the presence of water as solvent using the Onsager model. Only one starting conformation has been considered to perform all the calculations. Rigid energetic maps have been then constructed either by addition of diffuse or polarization functions to the basis set obtaining in that way 6-31+G(d)//6-31G(d), 6-31+G(d,p)//6-31G(d), and 6-311++G(d,p)//6-31G(d) energetic maps that have been carefully examined. The obtained structures corresponding to the lower energy conformers have been then fully optimized using different basis sets with the B3LYP method, a reversion in term of energy has been observed for the two first minima in the case of the charged disaccharide in the gas phase, this was attributed to the large grid of 30 degrees that could lead to the exclusion of an intermediate value corresponding to the real minimum of energy. We thus suggest that after establishing potential energy maps it is essential to proceed to full optimizations of the lower energy conformers. Calculations using the more accurate correlated method MP2 with the 6-31G(d) basis set have also been performed for conformers of the two disaccharides in the gas phase.

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Correlated ab initio quantum chemical calculations of di‐ and trisaccharide conformations

Cited by 9 publications

References 51 publications

Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Relaxed energetic maps of κ‐carrabiose: A DFT study

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