Instructions

In addition to these instructions there is also a more verbose manual.

1. General introduction
2. Sequence determination
3. Assignment of the spectrum of a known structure
4. Supported residues

General introduction

Recording of NMR spectra

NMR spectra should be recorded in D₂O at 70° and referenced against acetone (¹H 2.225 ppm, ¹³C 31.07 ppm) or 1,4-dioxane (¹³C 67.40 ppm). If a different reference has been used it may be necessary to correct the measured chemical shifts by subtraction of an offset. This is done by entering the correction in the field close to the chemical shifts. Differences in solvent or temperature are normally small (except for aromatic solvents, e.g. pyridine-d₅) and difficult to predict. If there is a large systematic error in the simulated spectrum this may be used as an approximate correction. However, this error depends on the structure from which it is taken and might not become zero after the first correction if an incomplete spectrum was used.

Sequence determination

Introduction

For a sequence determination You will require the results from a sugar (component) analysis, methylation (linkage) analysis and an NMR spectrum. The NMR data is entered manually in the form.

Step-by-step

1. Select residues from the pull-down menus.
   Note that some residues, such as methyl glycosides, are only available from the first menu.
2. Check the linkage positions. Some positions will not be available for certain sugars.
3. Select ¹³C or ¹H depending on data.
4. Enter the chemical shifts either in the text-area. The chemical shifts should be separated by spaces and/or linefeeds.
5. To save the content of the form first press the Save form button. You will now be able to download a form with all your selections as default values.
   Saving the filled-in form straight away will only result in a copy of the blank form.
6. Press Start simulation

Examples: dextran, a Shigella LPS, a Xylose containing N-glycan.

There is help available for the different elements of the form. This help is toggled on and off by pressing the ?-marks.

Assignment of a spectrum

Step-by-step

1. Select the appropriate residues. For a homopolymer a single residue may be sufficient but it must be selected from the first or last residue menu and linked using the self option.
   Note that some residues, such as methyl glycosides, are only available from the first menu.
2. Choose the anomeric configurations.
3. For each residue select the linkage type and the residue to which it is attached.
   Note that only residues on the first or last menu may be linked to them selves.
4. Enter the ¹H and ¹³C chemical shifts to be assigned (not required).
5. To save the content of the form first press the Save form button. You will now be able to download a form with all your selections as default values.
   Saving the filled-in form straight away will only result in a copy of the blank form.
6. Press Start simulation

Examples: Methyl b-D-cellobioside.

There is help available for the different elements of the form. This help is toggled on and off by pressing the ?-marks.

Appendix

Supported Residues

Residue Symbol Arabino-hexose 3,6-dideoxy-D- Tyvp (Tyvelose) Arabino-hexose 3,6-dideoxy-L- Ascp (Ascarylose) Ribo-hexose 3,6-dideoxy-D- Parp (Paratose) Xylo-hexose 3,6-dideoxy-D- Abep (Abequose) Xylo-hexose 3,6-dideoxy-L- Colp (Colitose) Abequose Abep Ascarylose Ascp Colitose Colp Fucopyranose D- D-Fucp Fucopyranose L- L-Fucp Galactopyranose 2-acetamido-2-deoxy-D- D-GalpNAc Galactopyranose 6-deoxy-D- D-Fucp (Fucose) Galactopyranose 6-deoxy-L- L-Fucp (Fucose) Galactopyranose D- D-Galp Galactopyranosiduronate D- D-GalpA Glucopyranose 2-acetamido-2-deoxy-D- D-GlcpNAc Glucopyranose 6-deoxy-D- D-Quip (Quinovose) Glucopyranose D- D-Glcp Glucopyranosiduronate D- D-GlcpA Mannopyranose 2-acetamido-2-deoxy-D- D-ManpNAc Mannopyranose 6-deoxy-D- D-Rhap (Rhamnose) Mannopyranose 6-deoxy-L- L-Rhap (Rhamnose) Mannopyranose D- D-Manp Mannopyranosiduronate D- D-ManpA Muramic acid MurNAc Paratose Parp Quinovose D- D-Quip Rhamnopyranose D- D-Rhap Rhamnopyranose L- L-Rhap Tyvelose Tyvp Made by: Magnus Lundborg