DOCSLIB.ORG

MM# Modeling of Aldopentose Pyranose Rings Michael K

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
MM# Modeling of Aldopentose Pyranose Rings Michael K Chemical and Biological Engineering Publications Chemical and Biological Engineering 2002 MM# Modeling of Aldopentose Pyranose Rings Michael K. Dowd United States Department of Agriculture William M. Rockey Iowa State University Alfred D. French United States Department of Agriculture See next page for additional authors Follow this and additional works at: http://lib.dr.iastate.edu/cbe_pubs Part of the Biochemical and Biomolecular Engineering Commons, and the Biological Engineering Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ cbe_pubs/31. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Chemical and Biological Engineering at Iowa State University Digital Repository. It has been accepted for inclusion in Chemical and Biological Engineering Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. MM# Modeling of Aldopentose Pyranose Rings Abstract MM3 (version 1992, ϵ=3.0) was used to study the ring conformations of d-xylopyranose, d-lyxopyranose and d-arabinopyranose. The nee rgy surfaces exhibit low-energy regions corresponding to chair and skew forms with high-energy barriers between these regions corresponding to envelope and half-chair forms. The lowest 4 energy conformer is C 1 for α- and β-xylopyranose and α- and β-lyxopyranose, and the lowest energy 1 conformer is C 4 for α- and β-arabinopyranose. Only α-lyxopyranose exhibits a secondary low-energy region 1 ( C 4) within 1 kcal/mol of its global minimum. Overall, the results are in good agreement with NMR and crystallographic results. For many of these molecules, skew conformations are found with relatively low 2 1 energies (2.5 to 4 kcal/mol above lowest energy chair form). The S O and C 4conformers of crystalline benzoyl derivatives of xylopyranose are in secondary low-energy regions on the β-xylopyranose surface, 4 within 3.8 kcal/mol of the global C 1 minimum. Disciplines Biochemical and Biomolecular Engineering | Biological Engineering | Chemical Engineering Comments This is a post-print of an article from Journal of Carbohydrate Chemistry, 21, no. 1–2 (2002): 11–25, doi: 10.1081/CAR-120003735. Authors Michael K. Dowd, William M. Rockey, Alfred D. French, and Peter J. Reilly This article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/cbe_pubs/31 MM3 MODELING OF ALDOPENTOSE PYRANOSE RINGS Michael K. Dowd,"·" William M. Rockey,ll Allred 0. French/' and Peter J. Reinyll asouthern Regional Research Center, ARS, USDA, 1100 Robert F.. Lee Blvd., New Orleans~ LA 70179, USA bDepartment of Chemical Engineering, Iowa State University, Ames) IA 50011~ USA ABSTRACT MM3 (version 1992, e = 3.0) was use.d to study the ring conformations of Dqxylopyranose, n­ lyxopyranose and D-arabinopyranose. The energy surfaces exhibit low-energy regions corresponding to chair and skew forms with high-energy barriers between these regions 4 corresponding to envelope and half-chair forms. The lowest energy conformer is C1 for a~ and 1 ~~-xylopyranose and a- and ~lyxopyranose, and the lowest energy conformer is c4 for a- and ~-arabinopyranose. Only a-lyxopyranose exhibits a secondary low-energy region ec-~) within 1 kcallmo! of its global minimum. Overa.Jl) the results are in good agreement with NMR and crystallographic results. For many of these molecules, skew conformations are found with 2 relatively low energies (2.5 to 4 kcal/mol above lowest energy chair form). The S0 and 'c~ conform<:rs of crystalline benzoyl derivatives ofxylopyranose axe in secondary low-tmergy 4 regions on the ~-xylopyranose surface, within 3.R kcat!moi of the global C1 minimum. 2 INTRODUCTION Previously, we modeled the pyranosy! ring shapes of the D-aldohexoses with the molecular mechanics progr.m1 MM3. 1 In general, MM3 predicted the shapes ofthes~ cydic structures well. AU of the p-anomers favored the 4C1 conformation, as did most of the a~anomcrs. For the hexoscs existing in multiple forms, e.g. a-idopyranosc and cx-aJtropyranose, the model predicted multiple forms. However, the conformer distribution predicted for these molecules was not always in exact agreement with the distributions predicted from NMR results, signifYing the effects of modeling error, including neglected solvation and entropic effects. In addition, a comparison of the predicted energies for the 'momers indicated that the equatorially configured P-structures were systematically ovcrprcdictcd. A better test of a potential energy function for predicting carbohydrate ring forms would be a series of pyranosyl structures known to be more variable in conformational preference. The aldopyranosyl pentoses, which lack the bulky hydroxymcthy1 group, represent such a series. By NMR,2..3 a.~ and p-xylopyranose and P-lyxopyranose exist predominately in the 4C1 fom1; a.- and ~-arabinopyranose exist predominately in the I ('4 form; and a-lyxopyranosc exists as a mixtur.: of the two chair forms. Ribopyranose, which has already been studied with MM3,4 is also found as a mixture of chair forms. This series appears to be a good test of the ability of potential functions to reproduce ring conformations. In addition to the goal of validating molecular models, there is interest in understanding how saccharides interact with proteins and how these interactions facilitate enzyme kinetics. in part, 3 this stems from the need to improve en:zyme stability or to alter reaction conditions. Xylanase is of commercial interest because it reduces the need for chlorine bleaching in paper pulping. 5.6 A number ofxylanase structures with xylan fragments or related derivatives bound to the active site have now been solved by diffraction crystallography, and these structures suggest that bound 7 9 xlyose rings can have non-chair conformations during hydrolysis. - An understanding of the confbnnational preferences of xylopyranose may be important for understanding the activity and specificity of these enzymes. METHODS The computational methods used in this work have been described in previous publications and 1 4 will only be outlined here. ' To be consistent with those calculations, the 1992 version of MM3 1o- 12 was used -with an elevated dielectric constant (e = 3.0). The elevated dielectric constant was used to reduce the strength of intramolecular hydrogen bonding and better mimic carbohydrates in condensed-phase systems. 13 Planar ring structures were initially generated with PC-Model (Serena Software, Bloomington, IN). These structures were then used to create puckered rings by moving three alternating ring atoms and their connected substituents perpendicular to the initial ring plane. This was accomplished by orienting the planar ring into the xy-plane and adjusting the z-coordinates of the atoms to be shifted. The atoms were moved over a runge of -0.8 A to +0.8 A in 0.1 A increments, which was sufficient to cover all likely ring shapes. For each riug, all three staggered gauche conformations of the four :secondary hydroxyl groups were also varied. Combined with the different combinations of ring shape, this yielded a total of 397,872 (173 x 3~) starting st.ru<.iures for each monosaccharide. Ring pucker was 4 maintained during the energy minimization by fixing the z-coordin.ates of the six ring atoms. All other degrees of freedom were allowed to relax. These optimizations were conducted with the block-diagonal Newton-R.aphson method (MM3 Option 1) and the default optimization criteria. The system of Cremer and Pople (q, ¢, 0) was used to quantify ring shape.14 From the full set of optimized structw'es, a Pickett-Strauss plate carrtle repre:>entation ( rA 0) of the Cremer and Pople puckering sphere was generatcd. 15 To construct this two-dimensional J .. representation, the data was sorted into 10° x J0° regions of¢ and 6, regardless of the value of q I ' or orientation of lhe individual exocyclic groups. The lowest energy conformer from each region was selected, and the resulting grid ofpoints was plotted using SURFER (Golden Software, Golden, CO). Positions of the characteristic conformers (chairs, boats, skews, etc.) within this two-dimensional space arc shown in Fig. 1. The Pickett-Strauss sur lace distorts some aspects of the puckering sphere. Most affected are the two poles {i.e. the chair conformers), which are transformed into the top and bottom y-axes. In effecl, the points representing the poles are stretched into lines corresponding to the two hori:1.ontnl boundaries. Because the system used to generate the puckered rings evenly samples the puckering sphere, the transformation results in a low density of data points near the two chair regions. This results in some distortion of the contour lines near these boundaries. To fmd local minima, the local low-energy regions were identified from the Pickett-strauss 4 surfaces. Molecules with these ring shnpes were built with all 81 (3 ) sets of staggered exocyclic orientations. All of these structures were freely optimi:1.ed to determine the lowest-energy form. 5 If any of the structures from one local region optimized to a different area of the puckering space, the region wa-. not considered to have a local minimum. The Karplus equations of Haasnoot et a1. 16 were used to calculate proton-proton coupling constants for these structures. The Cambridge Crystal Structure Database 17 was searched to identify related crystal structures. If there were multiple entries within the database, only the most recent determination was included in the analysis, and neutron diffraction determinations were used in preference to x-ray determinations. Structures for compounds containing L~sugars were included after converting the puckering parameters ( tPD = 180° - t/Jr. 01; """ 180° - Or) to account for the change in absolute configuration. The Protein Dala Bank 18 was searched tor stfU(,iures with bound xylose rings.
Load more

Recommended publications
  • Structural Features
    1 Structural features As defined by the International Union of Pure and Applied Chemistry gly- cans are structures of multiple monosaccharides linked through glycosidic bonds. The terms sugar and saccharide are synonyms, depending on your preference for Arabic (“sukkar”) or Greek (“sakkēaron”). Saccharide is the root for monosaccha- rides (a single carbohydrate unit), oligosaccharides (3 to 20 units) and polysac- charides (large polymers of more than 20 units). Carbohydrates follow the basic formula (CH2O)N>2. Glycolaldehyde (CH2O)2 would be the simplest member of the family if molecules of two C-atoms were not excluded from the biochemical repertoire. Glycolaldehyde has been found in space in cosmic dust surrounding star-forming regions of the Milky Way galaxy. Glycolaldehyde is a precursor of several organic molecules. For example, reaction of glycolaldehyde with propenal, another interstellar molecule, yields ribose, a carbohydrate that is also the backbone of nucleic acids. Figure 1 – The Rho Ophiuchi star-forming region is shown in infrared light as captured by NASA’s Wide-field Infrared Explorer. Glycolaldehyde was identified in the gas surrounding the star-forming region IRAS 16293-2422, which is is the red object in the centre of the marked square. This star-forming region is 26’000 light-years away from Earth. Glycolaldehyde can react with propenal to form ribose. Image source: www.eso.org/public/images/eso1234a/ Beginning the count at three carbon atoms, glyceraldehyde and dihydroxy- acetone share the common chemical formula (CH2O)3 and represent the smallest carbohydrates. As their names imply, glyceraldehyde has an aldehyde group (at C1) and dihydoxyacetone a carbonyl group (at C2).
    [Show full text]
  • Fall 2014 HO OH O OH O OH
    Fall 2014! HO OH O OH O OH HO OH HO OH !-D-ribofuranose (Haworth) HO HO O O HO OH OH HO HO OH !-D-mannopyranose HO OH (Haworth) anomeric anomeric carbon carbon The anomeric monosaccharides, α-D-glucopyranose and β-D-glucopyranose, drawn as Fischer and Haworth projections, and as ball-and-stick models Upon cyclization, the carbonyl carbon becomes chiral and is referred to as the anomeric carbon. In the α-form, the anomeric OH (O1) is on the opposite side of the ring from the CH2OH group, and in the β-form, O1 is on the same side. The α- and β-forms are referred to as anomers or anomeric pairs, and they interconvert in aqueous solution via the acyclic (“linear”) form (anomerization). Aqueous solutions of D-glucose contain ~64% β-pyranose and ~36% α-pyranose. OH OH O HO HO H O HO OH OH CHO OH OH !-D-glucopyranose OH OH 37.6 % !-D-glucofuranose HO 0.11 % OH OH OH OH OH O HO H HO D-glucose O OH HO OH acyclic aldehyde OH 0.006 % OH "-D-glucopyranose OH 62.0 % "-D-glucofuranose -H2O +H2O 0.28 % CH(OH)2 OH HO OH OH OH D-glucose acyclic hydrate 0.004 % Monosaccharides that are capable of assuming a form in solution that contains a free carbonyl group can be oxidized by relatively mild oxidizing agents such as Fe+3 or Cu+2 (Fehling’s reaction). The saccharide is oxidized and the reagent is reduced.! CHO COO- OH OH HO cyclic and hydrate HO forms of D-glucose OH OH 2Cu+2 2Cu+ OH OH OH OH D-glucose D-gluconate acyclic aldehyde q " Phosphorylation can restrict the types of cyclization reactions of the acyclic carbonyl form.
    [Show full text]
  • Structural and Functional Aspects of Pyranose-Furanose
    STRUCTURAL AND FUNCTIONAL ASPECTS OF PYRANOSE-FURANOSE MUTASES By Jijin Raj Ayanath Kuttiyatveetil A Thesis Submitted to the College of Graduate Studies and Research University of Saskatchewan In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Department of Chemistry, University of Saskatchewan, Saskatoon, SK, Canada © Jijin Raj Ayanath Kuttiyatveetil, May 2016. All rights reserved. Permission to Use In presenting this thesis in partial fulfillment of the requirements for a postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my work was completed. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in this thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Chemistry University of Saskatchewan Saskatoon, Saskatchewan (S7N 5C9) i Abstract Pyranose-Furanose mutases are enzymes that catalyze the isomerization of six-membered pyranose and five-membered furanose forms of a nucleotide-based sugar.
    [Show full text]
  • Biochemistry Prelude: Carbohydrates (Part-A)-Mono & Oligosaccharides
    Paper : 04 Metabolism of carbohydrates Module : 01 Prelude: Carbohydrates (Part-A) –Mono & Oligosaccharides Principal Investigator Dr.S.K.Khare,Professor IIT Delhi. Paper Coordinator Dr. Ramesh Kothari,Professor UGC-CAS Department of Biosciences Saurashtra University, Rajkot-5, Gujarat-INDIA Dr. S. P. SinghProfessor Content Reviewer UGC-CAS Department of Biosciences Saurashtra University, Rajkot-5, Gujarat-INDIA Dr. Ramesh Kothari,Professor UGC-CAS Department of Biosciences Content Writer Saurashtra University, Rajkot-5, Gujarat-INDIA 1 Metabolism of Carbohydrates Biochemistry Prelude: Carbohydrates (Part-A)-Mono & Oligosaccharides Description of Module Subject Name Biochemistry Paper Name 04 Metabolism of Carbohydrates Module Name/Title 01 Prelude: Carbohydrates (Part-A)- Mono & Oligosaccharides Dr. Vijaya Khader Dr. MC Varadaraj 2 Metabolism of Carbohydrates Biochemistry Prelude: Carbohydrates (Part-A)-Mono & Oligosaccharides PRELUDE-CARBOHYDRATES- (Monosaccharide’s and Oligosaccharides) Objectives 1. Introduction and the function of Functions of carbohydrates 2. To understand classification of carbohydrates 3. To study the characteristics of carbohydrates 4. To understand the properties of mono- and di- saccharides: 3 Metabolism of Carbohydrates Biochemistry Prelude: Carbohydrates (Part-A)-Mono & Oligosaccharides Introduction Carbohydrates are one of the three major macronutrients in our diet representing a wide group of substances which include the sugars, starches, glycogen, gums and celluloses. Carbohydrates are known as the important
    [Show full text]
  • 20H-Carbohydrates.Pdf
    Carbohydrates Carbohydrates are compounds that have the general formula CnH2nOn Because CnH2nOn can also be written Cn(H2O)n, they appear to be “hydrates of carbon” Carbohydrates are also called “sugars” or “saccharides” Carbohydrates can be either aldoses (ald is for aldehyde and ose means a carbohydrate) or ketoses (ket is for ketone) OH OH O OH CH2OH CH2OH OHC HOH2C OH OH OH OH An Aldose A Ketose (D-Glucose) (D-Fructose) Carbohydrates Due to the multiple chiral centers along a linear carbon chain for carbohydrates, Emil Fischer developed the “Fischer Projection” in order to represent these compounds Remember how to draw a Fischer projection: 1) View the linear carbon chain along the vertical axis (always place the more oxidized carbon [aldehyde in an aldose] towards the top) 2) The horizontal lines are coming out of the page toward the viewer 3) Will need to change the viewpoint for each carbon so the horizontal substituents are always pointing towards the viewer CHO OH OH H OH HO H CH2OH = OHC H OH OH OH H OH CH2OH Emil Fischer (1852-1919) Carbohydrates The aldoses are thus all related by having an aldehyde group at one end, a primary alcohol group at the other end, and the two ends connected by a series of H-C-OH groups CHO CHO CHO CHO CHO H OH H OH H OH H OH HO H CH2OH H OH H OH H OH HO H CH2OH H OH H OH HO H CH2OH H OH HO H CH2OH CH2OH Aldotriose Aldotetrose Aldopentose Aldohexose Aldohexose D-glyceraldehyde D-erythose D-ribose D-allose L-allose The D-aldoses are named according to glyceraldehyde, the D refers to the configurational
    [Show full text]
  • Molecular Dynamics Simulations of Forced Conformational Transitions in 1,6-Linked Polysaccharides
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector 1456 Biophysical Journal Volume 87 September 2004 1456–1465 Molecular Dynamics Simulations of Forced Conformational Transitions in 1,6-Linked Polysaccharides Gwangrog Lee,* Wies1aw Nowak,*z Justyna Jaroniec,* Qingmin Zhang,* and Piotr E. Marszalek*y *Department of Mechanical Engineering and Materials Science, yCenter for Bioinspired Materials and Material Systems, Duke University, Durham, North Carolina; and zInstitute of Physics, Nicholaus Copernicus University, Torun´, Poland ABSTRACT Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not fully understood. Here we use steered molecular dynamics simulations of the stretching process to unravel the mechanism of forced conformational transitions in 1,6 linked polysaccharides. In contrast to most sugars, 1,6 linked polysaccharides have an extra bond in their inter-residue linkage, C5–C6, around which restricted rotations occur and this additional degree of freedom increases the mechanical complexity of these polymers. By comparing the computational results with the atomic force microscopy data we determine that forced rotations around the C5–C6 bond have a significant and different impact on the elasticity of a- and b-linked polysaccharides. b-linkages of a polysaccharide pustulan force the rotation around the C5–C6 bonds and produce a Hookean-like elasticity but do not affect the conformation of the pyranose rings. However, a-linkages of dextran induce compound conformational transitions that include simultaneous rotations around the C5–C6 bonds and chair-boat transitions of the pyranose rings.
    [Show full text]
  • 25.3 Cyclization of Monosaccharides
    Hornback_Ch25_1085-1122 12/15/04 8:13 PM Page 1090 1090 CHAPTER 25 I CARBOHYDRATES PROBLEM 25.4 Determine the identity of each of these carbohydrates: O O CH2OH X X CH CH HO H HO H HO H HO H a) b) c) HO H HO H HO H CH2OH H OH H OH HO H CH X CH2OH O (Hint: This must be rotated first.) 25.3 Cyclization of Monosaccharides Up to this point, the structure of glucose has been shown as an aldehyde with hydroxy groups on the other carbons. However, as described in Section 18.9, aldehydes and ke- tones react with alcohols to form hemiacetals. When this reaction is intermolecular— that is, when the aldehyde group and the alcohol group are in different molecules—the equilibrium is unfavorable and the amount of hemiacetal that is present is very small. However, when the aldehyde group and the alcohol group are contained in the same molecule, as is the case in the second equation that follows, the intramolecular reaction is much more favorable (because of entropy effects; see Sections 8.13 and 18.9) and the hemiacetal is the predominant species present at equilibrium. H S O O . W Intermolecular reaction R±C±H ϩ H±.O .±R' R±C±H Equilibrium favors W reactants OS R' A hemiacetal H S O O H . Intramolecular reaction . O . OH Equilibrium favors products (6.7%) (93.3%) A cyclic hemiacetal Because glucose and the other monosaccharides contain both a carbonyl group and hy- droxy groups, they exist predominantly in the form of cyclic hemiacetals.
    [Show full text]
  • Hexose Permeation Pathways in Plasmodium Falciparum-Infected Erythrocytes
    Hexose permeation pathways in Plasmodium falciparum-infected erythrocytes Charles J. Woodrow, Richard J. Burchmore, and Sanjeev Krishna* Department of Infectious Diseases, St. George’s Hospital Medical School, Cranmer Terrace, London SW17 ORE, United Kingdom Edited by David Weatherall, University of Oxford, Oxford, United Kingdom, and approved June 21, 2000 (received for review April 5, 2000) Plasmodium falciparum requires glucose as its energy source to with PfHT1. This approach has been simultaneously applied to multiply within erythrocytes but is separated from plasma by GLUT1 to allow direct comparison between parasite and mam- multiple membrane systems. The mechanism of delivery of sub- malian transporters. strates such as glucose to intraerythrocytic parasites is unclear. We A complementary strategy to elucidate PfHT1 substrate– have developed a system for robust functional expression in protein interactions is based on mutational analysis. This has Xenopus oocytes of the P. falciparum asexual stage hexose per- already provided detailed mechanistic information when applied mease, PfHT1, and have analyzed substrate specificities of PfHT1. to other members of the major facilitator superfamily (5). We Ϸ We show that PfHT1 (a high-affinity glucose transporter, Km 1.0 mutated a highly phylogenetically conserved residue in helix 5 of Ϸ mM) also transports fructose (Km 11.5 mM). Fructose can replace PfHT1 that has been intensively studied in homologues (6, 7). glucose as an energy source for intraerythrocytic parasites. PfHT1 These findings combined with previous studies demonstrate binds fructose in a furanose conformation and glucose in a pyr- topological conservation among hexose transporters but also anose form. Fructose transport by PfHT1 is ablated by mutation of confirm important mechanistic differences between phylo- a single glutamine residue, Q169, which is predicted to lie within genetically diverse organisms.
    [Show full text]
  • Glucose Hemi-Acetal & Acetal (Glyoside) Formation: Some
    GLUCOSE HEMI-ACETAL & ACETAL (GLYOSIDE) FORMATION: SOME COMMON CONCEPTS IN CARBOHYDRATE (“SUGAR”) CHEMISTRY Carbohydrates • (carbon + hydrate) are molecules with three or more carbons and a general formula that approximates CnH2nOn Saccharides • are carbohydrates or sugars • monosaccharides have one sugar moiety • disaccharides have two sugars linked together • trisaccharides have three sugars linked together • tetrasaccharides have four sugars linked together, etc... • polysaccharides have an indeterminate number which can be hundreds of thousands or more Prefixes and Suffixes • the suffix (ending) for sugar names is: -ose • the prefix defines the number of carbons: o triose (3 carbons) o tetrose (4 carbons) o pentose (5 carbons) o hexose (6 carbons), etc… • a further prefix defines the types of carbonyl group in the sugar: o aldo- (aldehyde) or o keto- (ketone) o for example glucose (shown below) is an "aldohexose" whereas fructose is a "ketohexose" • the term pyranose means a six-membered sugar ring (hemiacetal or acetal - see below) • the term furanose means a five-membered ring • These terms are often prefixed as in "glucopyranose" which means glucose cyclized to its six-membered ring form (see below) Intro Chem Handouts Carbohydrate Chemistry Page 1 of 4 D- and L- Sugars • This is a naming convention • Using standard nomenclature numbering, determine the configuration (R or S) of the highest numbered stereogenic center ("chiral center" or "asymmetric center"): o if it has R-configuration, the sugar is a D-sugar o if it has S-configuration, the sugar is an L-sugar Glucose Hemi-Acetal Formation • The open form of D-glucose (and many other sugars) can cyclize to form hemiacetals.
    [Show full text]
  • Drawing Sugar Structures: Fischer Projections, Haworth Structures and Chair Conformers
    Drawing Sugar Structures: Fischer Projections, Haworth Structures and Chair Conformers The acyclic structure of a sugar is commonly drawn as a Fischer projection. These structures make it easy to show the configuration at each stereogenic center in the molecule without using wedges and dashes. Fischer projections also allow an easy classification of the sugar as either the D-enantiomer or the L-enantiomer. Both the line-angle structure and the Fischer projection of the aldohexose D-allose are shown below. Cyclic Hemiacetal Formation Aldoses contain an aldehyde group and hydroxyl groups, and they undergo intramolecular reactions to form cyclic hemiacetals. These five-membered and six-membered cyclic hemiacetals are often more stable than the open-chain form of the sugar. In D-allose, nucleophilic attack on the carbonyl carbon of the aldehyde group by the hydroxyl group on carbon five (C-5) gives a six-membered ring cyclic hemiacetal. The new bond that forms between the oxygen atom on C-5 and the hemiacetal carbon atom C-1 is usually shown by using a box in the Fischer projection. This cyclic structure is called the pyranose ring form of the sugar. When the cyclic hemiacetal forms, the C-1 carbon atom becomes a new stereogenic center and can have either an R- or an S-configuration. To illustrate the ambiguity in the configuration at this new stereogenic center, squiggly lines are used in the Fischer projection to connect the hydrogen and the hydroxyl group to C-1. A Fischer projection can illustrate the structure of the cyclic hemiacetal form of a sugar, but it lacks something aesthetically as far as representing the six-membered ring in the structure.
    [Show full text]
  • FOOD300010 Revision Questions
    FOOD30010: Carbohydrate Study Questions Fructose * NB: for fructose, C1 and C6 (at each ends) are primary alcohol (CH2OH) — i.e. NO primary aldehyde 1. Know how to draw the Fisher Projection and Haworth structure of: Glucose, mannose, galactose and - furanose is formed from the reaction of C2-ketone with C5-OH *fructofuranose form is more stable fructose. - pyranose is formed from the reaction of C2-ketone with C6-OH The cyclisation of keto-sugar (fructose) involves the creation between a ketone and an alcohol, thus forming weak hemiketal bond. Fructofuranose is much sweeter than fructopyranose when out from the oven. The sugar favours fructofuranose form more in lower temperatures, thus the cake’s taste is increased significantly after being cooled. - In the Fischer projection, we can see that the monosaccharides contain aldehyde group (CHO) on one end, Hydrogen atoms (H) and hydroxyl groups (OH) in the middle section, and a primary alcohol group (CH2OH) on the other end. - NB: for D-aldo sugars family, the hydroxy (OH) group next to the primary alcohol (at the bottom) is positioned on the right. Reaction between sugars to build larger units - alcohol can react with hemiacetal or hemiketal of sugars to form strong glycosidic bond by a dehydration reaction - the glycosidic linkage formed can either be alpha- or beta- linkages 2. Be able to give example pair of sugars to illustrate the following: - the configuration of a glycosidic linkage is fixed i) Structural isomers • compounds with the same molecular formula but with atoms arranged
    [Show full text]
  • Atomic Levers Control Pyranose Ring Conformations
    Proc. Natl. Acad. Sci. USA Vol. 96, pp. 7894–7898, July 1999 Biophysics Atomic levers control pyranose ring conformations PIOTR E. MARSZALEK†‡,YUAN-PING PANG§,HONGBIN LI‡,JAMAL EL YAZAL§,ANDRES F. OBERHAUSER‡, AND JULIO M. FERNANDEZ†‡ ‡Department of Physiology and Biophysics, §Mayo Clinic Cancer Center, Department of Pharmacology, Mayo Foundation, Rochester, MN 55905 Edited by Jiri Jonas, University of Illinois at Urbana–Champaign, Urbana, IL, and approved May 18, 1999 (received for review March 12, 1999) ABSTRACT Atomic force microscope manipulations of single polysaccharide molecules have recently expanded con- formational chemistry to include force-driven transitions between the chair and boat conformers of the pyranose ring structure. We now expand these observations to include chair inversion, a common phenomenon in the conformational chemistry of six-membered ring molecules. We demonstrate that by stretching single pectin molecules (1 3 4-linked ␣-D-galactouronic acid polymer), we could change the pyr- anose ring conformation from a chair to a boat and then to an 4 inverted chair in a clearly resolved two-step conversion: C1 i 1 boat i C4. The two-step extension of the distance between the glycosidic oxygen atoms O1 and O4 determined by atomic force microscope manipulations is corroborated by ab initio calcu- lations of the increase in length of the residue vector O1O4 on chair inversion. We postulate that this conformational change results from the torque generated by the glycosidic bonds when a force is applied to the pectin molecule. Hence, the FIG. 1. A simplified mechanical model of the pyranose ring. An external force (F) is applied to the ring through the oxygen atoms O glycosidic bonds act as mechanical levers, driving the confor- 1 and O4 as in an (1a 3 4e)-linked polysaccharide chain (e.g., amylose).
    [Show full text]