The Application of Molecular Modeling Techniques to the Determination of Oligosaccharide Solution Conformations

Woods, Robert J.

doi:10.1002/9780470125861.ch3

Cited by 22 publications

(11 citation statements)

References 148 publications

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“…Negative hyperconjugation can be subdivided into some special cases, of which we will mention specifically the Bohlmann effect [4c, 35,36], and the anomeric effect [4d, [37][38][39]. Each of these is well known, and numerous papers including quite a few reviews have been written on them.…”

Section: Negative Hyperconjugationmentioning

confidence: 98%

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Understanding molecular structure from molecular mechanics

Allinger

2011

J Comput Aided Mol Des

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Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

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Section: Negative Hyperconjugationmentioning

confidence: 98%

“…The gauche form has a lone pair anti to the methyl c See footnote to manuscript title originally in carbohydrates, and later it was extended to many other classes of compounds. This one is called the anomeric effect [4d, [37][38][39].…”

Section: Bohlmann Effectmentioning

confidence: 99%

Understanding molecular structure from molecular mechanics

Allinger

2011

J Comput Aided Mol Des

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“…119,120 In contrast, the conformational states of oligosaccharides have been well characterized (often from NMR studies or small-molecule crystallography) and appear to be guided by well-defined and predictable rules. Understanding these rules, as summarized in the essential reference Conformations of Carbohydrates, 121 and the underlying physics 45,122–124 has enabled accurate force fields for carbohydrate modeling to be created. 14,20,25–39 However, from a modeling perspective, the most significant property of oligosaccharides is that two-bond glycosidic linkages between pyranose rings predominantly populate only a single conformation.…”

Section: First-principles Predictions Of Oligosaccharide Conformationsmentioning

confidence: 99%

Predicting the Structures of Glycans, Glycoproteins, and Their Complexes

2018

Self Cite

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Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.

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“…These become especially important in polysaccharides, 22 and an example will be discussed in the following section. These become especially important in polysaccharides, 22 and an example will be discussed in the following section.…”

Section: Glucose Diastereomersmentioning

confidence: 99%

“…(The latter calculations could, of course, be improved by using an MP2 or other better correlation calculation in place of B3LYP, and by optimizing the geometry at the same time, instead of a single point, but that was not feasible at the time this work was done.) 22 Whether or not additional effects will be found in oligosaccharides beyond those known in disaccharides has yet to be established. This fi gure is a fairly good example of the accuracy and transferability of potential functions that can be obtained with molecular mechanics.…”

Section: External Anomeric Torsional Effectmentioning

confidence: 99%

Additional Stereochemical Effects in Carbohydrates

Allinger¹

2010

Molecular Structure

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The Application of Molecular Modeling Techniques to the Determination of Oligosaccharide Solution Conformations

Cited by 22 publications

References 148 publications

Understanding molecular structure from molecular mechanics

Understanding molecular structure from molecular mechanics

Predicting the Structures of Glycans, Glycoproteins, and Their Complexes

Additional Stereochemical Effects in Carbohydrates

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