Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software

Size: px
Start display at page:

Download "Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software"

Transcription

1 Supporting Information Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software Roman R. Kapaev*, and Philip V. Toukach*, Higher Chemical College of the Russian Academy of Sciences, Miusskaya sq. 9, Moscow , Russia N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow , Russia * Corresponding authors: Roman R. Kapaev <kapaev_roman@mail.ru>, Philip V. Toukach <netbox@toukach.ru> ABSTRACT: Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of 1 H and 13 C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated 1 H and 13 C chemical shifts in the form of most 2D spin correlation spectra commonly used in carbohydrate research, such as 1 H- 1 H TOCSY, COSY/COSY-DQF/COSY-RCT and 1 H- 13 C edhsqc, HSQC-COSY, HSQC-TOCSY, and HMBC. Peaks in the simulated 2D spectra are color-coded and labeled according to the signal assignment, and can be exported in JCAMP-DX format. Peak widths are estimated empirically from the structural features. GODESS is available free of charge via the Internet at the platform of the Carbohydrate Structure Database (CSDB) project ( Page S-1

2 Section 1. Peak width estimation algorithm. Each 1 H chemical shift is given a width index I w. The peak width (PW, in Hz), is roughly estimated basing on typical values of spin coupling constants in carbohydrates and derivatives. 1-5 PW values are calculated according to the formula: = 3 The numerical term (3 Hz) is a step of coupling constant estimation, which was chosen to obtain 3-4 grades of spin-spin coupling range within 2-15 Hz. The I w is calculated as a sum of the following terms: 1. Geminal spin-spin coupling term a. is equal to 1 for geminal protons attached to sp 2 -carbons b. is equal to 3 for geminal protons attached to sp 3 -carbons c. is equal to 0 for non-geminal protons 2. Spin-spin couplings with vicinal protons (all vicinal protons are divided into groups, each group includes all atoms linked to the same carbon and is considered independently): a. in case the interacting protons are exocyclic I. is equal to 3 if both the current (simulated proton) and its vicinal protons are attached to sp 2 -carbons (e.g., H9-H10 of oleic acid) II. is equal to 2 if the current and/or its vicinal proton are attached to sp 3 -carbons (e.g., protons of stearic acid, ribitol, H6-H7 of ᴅ-glycero-ʟ-manno-heptose) b. in case the interacting protons are endocyclic I. if there is only one vicinal proton in a group, for furanose residues i. is equal to 2 if the current and the vicinal protons are in cis-configuration (e.g., tagatofuranose H3-H4) ii. is equal to 3 if the current and the vicinal protons are in transconfiguration (e.g., fructofuranose H3-H4) iii. is equal to 2.5 if the current proton has a geminal neighbor (e.g., tyvelose H3/H3 with H2 vicinal). In this case, I w = 2 for the one (cis) and I w = 3 for the other (trans) methylene proton. Mapping between these two crosspeaks and these two protons is impossible, so the values are averaged. iv. is equal to 1 in any other case (e.g., double bond) II. if there is only one vicinal proton in a group, for pyranose residues i. is equal to 3 if both protons are axial (e.g., Glcp H2-H3) ii. is equal to 1 if at least one of the protons is equatorial (e.g., α-glcp H1- H2, Manp H2-H3, Arap H5-H6/H6 with H5 vicinal) iii. is equal to 2 if the current proton has a geminal neighbor and the vicinal proton is axial (e.g., tyvelose H3/H3 with H2 vicinal). In this case, I w = 1 for the one (ax-eq) and I w = 3 for the other (ax-ax) methylene proton. Mapping between these two cross-peaks and these two protons is impossible, so the values are averaged. iv. is equal to 1 in any other case (e.g., double bond) III. is equal to 4 for pyranose and to 5 for furanose residues if there are two vicinal protons in a group (e.g., tyvelose H2 with deoxy H3/H3 vicinal) c. in case the interacting protons are both endo- and exocyclic I. is equal to 1 if there is only one vicinal proton in a group (e.g., Glc H6 with H5 vicinal, pseudaminic acid H6 with H7 vicinal) II. is equal to 2 if there are three vicinal protons in a group, implying a methyl group (e.g., rhamnopyranose H5 with H6 vicinal) III. is equal to 3 if there are two vicinal protons in a group (e.g., Glc H5 with H6 vicinal) d. is equal to 0 if there are no vicinal protons (e.g., fructofuranose H1) Along the 13 C axis, every cross-peak is considered 125 Hz wide, which is a typical value in heteronuclear 2D NMR spectra. Page S-2

3 Figure S1. GODESS structure input interface: (1) structure input options, (2) CSDB linear code input field, (3) simulation settings (clicking More parameters checkbox shows/hides the additional parameters). Figure S2. Residue assignment (a) and trustworthiness (b) visualization modes for the COSY spectrum of sucrose. In the assignment mode, glucose residue peaks are plotted in red and fructose peaks are plotted in green; the labels represent the signal assignment to atoms. In the trustworthiness mode, the greener peak stands for the more accurate simulation; the labels are a numeric metric of trustworthiness. Page S-3

4 Figure S3. edhsqc spectrum of sucrose (residue assignment visualization mode). Negative peaks are shown as rectangles and positive ones are shown as ellipses. Glucose residue peaks are plotted in red and fructose peaks are plotted in green. Figure S4. HMBC spectrum of sucrose (residue assignment visualization mode). Glucose residue peaks are plotted in red and fructose peaks are plotted in green. The inter-residue peak between glucose H1 and fructose C2 is plotted using both colors. Page S-4

5 Figure S5. Options available by mouse hovering over JDX. Clicking Live view NMR opens the cheminfo.org online 2D NMR viewer (see Figure S6). Figure S6. Simulated HSQC spectrum of α-lactose opened in the cheminfo.org online 2D NMR viewer. Page S-5

6 Figure S7. Simulated HSQC spectra of lactose (α-lactose, red; β-lactose, blue) exported to JCAMP-DX file and viewed in MestreNova in superposition with experimental HSQC spectrum of lactose. The experimental spectrum with slightly different recording options was adapted with DSS/TMS correction from record ID bmse in Biological Magnetic Resonance Data Bank 6. Page S-6

7 Figure S8. Experimental (black) and simulated (red) COSY spectra of the O-polysaccharide from Citrobacter freundii O22 strain PCM Figure S9. Experimental (black) and simulated (red) HSQC spectra of the O-polysaccharide from Proteus mirabilis G1. Page S-7

8 Figure S10. Experimental (black) and simulated (red) TOCSY spectra portions of Streptococcus suis serotype 2 capsular polysaccharide. Page S-8

9 References 1. Pretsch, E.; Bühlmann, P.; Affolter, C. In Structure determination of organic compounds; Pretsch, E.; Bhuhlmann, P.; Affolter, C., Ed.; Springer-Verlag Berlin Heidelberg: 2009; Vol. 13., Chapter 5, pp Altona, C.; Haasnoot, C. A., Prediction of Anti and Gauche Vicinal Proton Proton Coupling Constants in Carbohydrates: a Simple Additivity Rule for Pyranose Rings. Org. Magn. Resonance 1980, 13, De Leeuw, F. A.; Altona, C., Computer Assisted Pseudorotation Analysis of Five Membered Rings by Means of Proton Spin Spin Coupling Constants: Program PSEUROT. J. Comput. Chem. 1983, 4, Olson, W. K.; Sussman, J. L., How Flexible is the Furanose Ring? 1. A Comparison of Experimental and Theoretical Studies. J. Am. Chem. Soc. 1982, 104, Stenutz, R.; Carmichael, I.; Widmalm, G.; Serianni, A. S., Hydroxymethyl Group Conformation in Saccharides: Structural Dependencies of 2 J HH, 3 J HH, and 1 J CH Spin-Spin Coupling Constants. J. Org. Chem. 2002, 67, Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.; Harano, Y.; Ioannidis, Y. E.; Lin, J.; Livny, M.; Mading, S.; Maziuk, D.; Miller, Z., BioMagResBank. Nucl. Acids Res. 2008, 36, D402-D408. Page S-9

Determining Chemical Structures with NMR Spectroscopy the ADEQUATEAD Experiment

Determining Chemical Structures with NMR Spectroscopy the ADEQUATEAD Experiment Determining Chemical Structures with NMR Spectroscopy the ADEQUATEAD Experiment Application Note Author Paul A. Keifer, Ph.D. NMR Applications Scientist Agilent Technologies, Inc. Santa Clara, CA USA Abstract

More information

NMR Predictor. Introduction

NMR Predictor. Introduction NMR Predictor This manual gives a walk-through on how to use the NMR Predictor: Introduction NMR Predictor QuickHelp NMR Predictor Overview Chemical features GUI features Usage Menu system File menu Edit

More information

Supplementary Information. Glycosylation of a model proto-rna nucleobase with non-ribose sugars: Implications o the prebiotic synthesis of nucleosides

Supplementary Information. Glycosylation of a model proto-rna nucleobase with non-ribose sugars: Implications o the prebiotic synthesis of nucleosides Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry. This journal is The Royal Society of Chemistry 2018 Supplementary Information Glycosylation of a model proto-rna nucleobase

More information

Module 20: Applications of PMR in Structural Elucidation of Simple and Complex Compounds and 2-D NMR spectroscopy

Module 20: Applications of PMR in Structural Elucidation of Simple and Complex Compounds and 2-D NMR spectroscopy Subject Chemistry Paper No and Title Module No and Title Module Tag Paper 12: Organic Spectroscopy Module 20: Applications of PMR in Structural Elucidation of Simple and Complex Compounds and 2-D NMR spectroscopy

More information

F.V. Toukach. Methods of 1D and 2D NMR in structural elucidation of natural glycopolymers

F.V. Toukach. Methods of 1D and 2D NMR in structural elucidation of natural glycopolymers F.V. Toukach Methods of D and 2D NMR in structural elucidation of natural glycopolymers Choice of the demo material In genomics and proteomics primary structure elucidation is more automatized In glycomics:

More information

Basic One- and Two-Dimensional NMR Spectroscopy

Basic One- and Two-Dimensional NMR Spectroscopy Horst Friebolin Basic One- and Two-Dimensional NMR Spectroscopy Third Revised Edition Translated by Jack K. Becconsall WILEY-VCH Weinheim New York Chichester Brisbane Singapore Toronto Contents XV 1 The

More information

COSY type experiments exploring through-bond homonuclear correlations

COSY type experiments exploring through-bond homonuclear correlations COSY type experiments exploring through-bond homonuclear correlations Assistant Professor Kenneth Kongstad Bioanalytical Chemistry and Metabolomics Research Group Section for Natural Products and Peptides

More information

Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts

Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts pubs.acs.org/jcim Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts Roman R. Kapaev, Ksenia S. Egorova,*, and Philip V.

More information

(b) How many hydrogen atoms are in the molecular formula of compound A? [Consider the 1 H NMR]

(b) How many hydrogen atoms are in the molecular formula of compound A? [Consider the 1 H NMR] CHEM 6371/4511 Name: The exam consists of interpretation of spectral data for compounds A-C. The analysis of each structure is worth 33.33 points. Compound A (a) How many carbon atoms are in the molecular

More information

Tools for Structure Elucidation

Tools for Structure Elucidation Innovation with Integrity Tools for Structure Elucidation Sandra Groscurth Workflow in Natural Product Research Organism Natural Products Extraction Activity Assay Characterization of Unknown Structures

More information

Spin-spin coupling I Ravinder Reddy

Spin-spin coupling I Ravinder Reddy Spin-spin coupling I Ravinder Reddy Spin-interactions External interactions Magnetic field Bo, RF field B1 Internal Interactions Molecular motions Exchange Chemical shifts J-coupling Spin Diffusion Dipolar

More information

Biochemistry 530 NMR Theory and Practice. Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington

Biochemistry 530 NMR Theory and Practice. Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington Biochemistry 530 NMR Theory and Practice Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington 1D spectra contain structural information.. but is hard to extract:

More information

The wonderful world of NUCLEIC ACID NMR!

The wonderful world of NUCLEIC ACID NMR! Lecture 12 M230 Feigon Sequential resonance assignments in DNA (and RNA): homonuclear method 2 structure determination Reading resources Evans Chap 9 The wonderful world of NUCLEIC ACID NMR! Catalytically

More information

Supporting Information

Supporting Information Supporting Information German Edition: DOI: Posttranslational Modifications of Intact Proteins Detected by NMR Spectroscopy: Application to Glycosylation** Mario Schubert,* Michal J. Walczak,* Markus Aebi,

More information

The Final Learning Experience

The Final Learning Experience Chemistry 416 Spectroscopy Fall Semester 1997 Dr. Rainer Glaser The Final Learning Experience Monday, December 15, 1997 3:00-5:00 pm Name: Answer Key Maximum Question 1 (Combination I) 20 Question 2 (Combination

More information

Nuclear Magnetic Resonance Spectroscopy

Nuclear Magnetic Resonance Spectroscopy 13 Nuclear Magnetic Resonance Spectroscopy Solutions to In-Text Problems 13.1 (b) Apply Eq. 13.2b with = 360 MHz. chemical shift in Hz = δ = (4.40)(360) = 1584 Hz 13.2 (b) Follow the same procedure used

More information

NMR Studies of a Series of Shikimic Acid Derivatives

NMR Studies of a Series of Shikimic Acid Derivatives Journal of the Chinese Chemical Society, 2007, 54, 1313-1320 1313 NMR Studies of a Series of Shikimic Acid Derivatives Ping Zhang ( ), Jian Huang ( ) and Fen-Er Chen* ( ) Department of Chemistry, Fudan

More information

Non Uniform Sampling in Routine 2D Correlation Experiments

Non Uniform Sampling in Routine 2D Correlation Experiments Analytical and Imaging Solutions for Advanced R&D Non Uniform Sampling in Routine 2D Correlation Experiments NUCLEAR MAGNETIC RESONANCE INTRODUCTION Data obtained from two-dimensional NMR experiments is

More information

Chem 215 F11 Notes Dr. Masato Koreeda - Page 1 of 18. Date: November 9, 2011

Chem 215 F11 Notes Dr. Masato Koreeda - Page 1 of 18. Date: November 9, 2011 Chem F Notes Dr. Masato Koreeda - Page of 8. Date: November 9, 0 Chapters.8; -,,, and 7: Carbohydrates Part I Carbohydrate nomenclature: http://www.chem.qmul.ac.uk/iupac/carb/ Carbohydrates: Polyhydroxylated

More information

2D NMR: HMBC Assignments and Publishing NMR Data Using MNova

2D NMR: HMBC Assignments and Publishing NMR Data Using MNova Homework 10 Chem 636, Fall 2014 due at the beginning of lab Nov 18-20 updated 10 Nov 2014 (cgf) 2D NMR: HMBC Assignments and Publishing NMR Data Using MNova Use Artemis (Av-400) or Callisto (Av-500) for

More information

NMR spectra of some simple molecules. Effect of spinning: averaging field inhomogeneity (nmr1.pdf pg 2)

NMR spectra of some simple molecules. Effect of spinning: averaging field inhomogeneity (nmr1.pdf pg 2) NMR spectra of some simple molecules Effect of spinning: averaging field inhomogeneity (nmr1.pdf pg 2) N S H 0 H o Because the protons have a magnetic field associated with them, the field changes as across

More information

Origin of Scalar Couplings BCMB/CHEM 8190

Origin of Scalar Couplings BCMB/CHEM 8190 Origin of Scalar Couplings BCMB/CHEM 8190 Traditional View of Scalar Coupling Splitting of NMR signals due to through-bond interactions between nuclei is called scalar coupling (or J coupling or through-bond

More information

Reassignment of the 13 C NMR spectrum of minomycin

Reassignment of the 13 C NMR spectrum of minomycin Reassignment of the 13 C NMR spectrum of minomycin Yoshito Takeuchi*, Yoko Imafuku, and Miki Nishikawa Department of Chemistry, Faculty of Science, Kanagawa University 2946 Tsuchiya, Hiratsuka, Japan 259-1293

More information

1 st -order spin-spin coupling. 2 nd -order spin-spin coupling. ν/j < 10

1 st -order spin-spin coupling. 2 nd -order spin-spin coupling. ν/j < 10 1 st -order spin-spin coupling We observe 1 st -order NMR spectra when the frequency difference between the chemical shifts of any given pair of nuclei is much larger than the value of the coupling constant

More information

Experience the most powerful benchtop NMR spectrometer

Experience the most powerful benchtop NMR spectrometer Experience the most powerful benchtop NMR spectrometer Outstanding Features Highest field strength (80 MHz) Largest chemical shift spread Highest sensitivity Superb Resolution (0.5 Hz/20 Hz) Multi-nuclear

More information

NMRis the most valuable spectroscopic technique for organic chemists because it maps the carbon-hydrogen framework of a molecule.

NMRis the most valuable spectroscopic technique for organic chemists because it maps the carbon-hydrogen framework of a molecule. Chapter 13: Nuclear magnetic resonance spectroscopy NMRis the most valuable spectroscopic technique for organic chemists because it maps the carbon-hydrogen framework of a molecule. 13.2 The nature of

More information

(Refer Slide Time: 0:37)

(Refer Slide Time: 0:37) Principles and Applications of NMR spectroscopy Professor Hanudatta S. Atreya NMR Research Centre Indian Institute of Science Bangalore Module 3 Lecture No 14 We will start today with spectral analysis.

More information

Module 13: Chemical Shift and Its Measurement

Module 13: Chemical Shift and Its Measurement Subject Chemistry Paper No and Title Module No and Title Module Tag Paper 12: Organic Spectroscopy CHE_P12_M13_e-Text TABLE OF CONTENTS 1. Learning Outcomes 2. Introduction 3. Shielding and deshielding

More information

Supporting Information

Supporting Information S1 Supporting Information The Five - and Six -Membered Conformationally- Locked 2',4'-Carbocyclic ribo-thymidine: Synthesis, Structure and Biochemical Studies Puneet Srivastava, Jharna Barman, Wimal Pathmasiri,

More information

BCMB/CHEM 8190 Lab Exercise Using Maple for NMR Data Processing and Pulse Sequence Design March 2012

BCMB/CHEM 8190 Lab Exercise Using Maple for NMR Data Processing and Pulse Sequence Design March 2012 BCMB/CHEM 8190 Lab Exercise Using Maple for NMR Data Processing and Pulse Sequence Design March 2012 Introduction Maple is a powerful collection of routines to aid in the solution of mathematical problems

More information

NMR at UNC: Tips, Tricks, and Techniques

NMR at UNC: Tips, Tricks, and Techniques NMR at UNC: Tips, Tricks, and Techniques Laura Adduci UNC-Chapel Hill Graduate student Gagné Lab NMR Assistant Chemistry Department Topics and Examples 1. 2D spectra 2. Selective 1D spectra 3. Homonuclear

More information

KEY I. (28 points) i) NOTE: sp-hybridized carbanions make good nucleophiles for substitution reactions. Product A C C CH 3. Product B.

KEY I. (28 points) i) NOTE: sp-hybridized carbanions make good nucleophiles for substitution reactions. Product A C C CH 3. Product B. I. (8 points) Page 1 A. omplete the following as necessary NT: sp-hybridized carbanions make good nucleophiles for substitution reactions NaN N Na Na (optional) i equivalents of Product A Product B a)

More information

Protein NMR. Bin Huang

Protein NMR. Bin Huang Protein NMR Bin Huang Introduction NMR and X-ray crystallography are the only two techniques for obtain three-dimentional structure information of protein in atomic level. NMR is the only technique for

More information

Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy

Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy Murphy, B. (2017). Fluorescence and Nuclear Magnetic Resonance Spectroscopy: Lecture 3. Lecture presented at PHAR 423 Lecture in UIC College

More information

Nuclear Magnetic Resonance

Nuclear Magnetic Resonance Nuclear Magnetic Resonance Most of you should have learned about NMR in your organic course. Just to underscore that learning, let me say that NMR is arguably the best technique we have for characterizing

More information

NMR NEWS June To find tutorials, links and more, visit our website

NMR NEWS June To find tutorials, links and more, visit our website Department of Chemistry NMR Facilities Director: Dr. Carlos A. Steren NMR NEWS June 2014 To find tutorials, links and more, visit our website www.chem.utk.edu/facilities/nmr Computers and software updates

More information

NMR parameters intensity chemical shift coupling constants 1D 1 H spectra of nucleic acids and proteins

NMR parameters intensity chemical shift coupling constants 1D 1 H spectra of nucleic acids and proteins Lecture #2 M230 NMR parameters intensity chemical shift coupling constants Juli Feigon 1D 1 H spectra of nucleic acids and proteins NMR Parameters A. Intensity (area) 1D NMR spectrum: integrated intensity

More information

Chapter 15 Lecture Outline

Chapter 15 Lecture Outline Organic Chemistry, First Edition Janice Gorzynski Smith University of Hawaii Chapter 5 Lecture Outline Introduction to NMR Two common types of NMR spectroscopy are used to characterize organic structure:

More information

Please read and sign the Honor Code statement below:

Please read and sign the Honor Code statement below: CHEM 3311 Exam #2 Name Dr. Minger June 16, 2014 Please read and sign the Honor Code statement below: I pledge that on my honor, as a University of Colorado at Boulder student, I have neither given nor

More information

Homework 6 Organic Chemistry MCAT Review Summer 2012 Brent Iverson

Homework 6 Organic Chemistry MCAT Review Summer 2012 Brent Iverson omework 6 rganic hemistry MAT Review Summer 2012 Brent Iverson 1 1. Fill in each blank with the word that best completes the following sentences about NMR. The two most important isotopes for organic chemistry

More information

Supplementary Materials for

Supplementary Materials for advances.sciencemag.org/cgi/content/full/3/8/e1701126/dc1 Supplementary Materials for A polyaromatic nanocapsule as a sucrose receptor in water Masahiro Yamashina, Munetaka Akita, Taisuke Hasegawa, Shigehiko

More information

1,1,2-Tribromoethane. Spin-Spin Coupling

1,1,2-Tribromoethane. Spin-Spin Coupling NMR Spin oupling Spin-Spin oupling Spectra usually much more complicated than a series of single lines, one for each type of hydrogen. Peaks are often split into a number of smaller peaks, sometimes with

More information

Spin mixing at level anti-crossings in the rotating frame makes high-field SABRE feasible

Spin mixing at level anti-crossings in the rotating frame makes high-field SABRE feasible Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2014 Electronic Supplementary Information for the article Spin mixing at level anti-crossings

More information

StepNOESY Overcoming Spectral Overlap in NOESY1D

StepNOESY Overcoming Spectral Overlap in NOESY1D StepNOESY Overcoming Spectral Overlap in NOESY1D Application Note Author David Russell NMR Applications Scientist Research Products Group Santa Clara, CA Abstract VnmrJ 3 software provides easy-to-use,

More information

H-C one-bond correlations: HSQC Preliminaries.

H-C one-bond correlations: HSQC Preliminaries. A. F. Miller 2010 C HSQC H-C one-bond correlations: HSQC Preliminaries. For both 1 H and C, you need a good power pw90 pair and you should have good values for both sw and tof for both nuclei. In short,

More information

CM Chemical Spectroscopy and Applications. Final Examination Solution Manual AY2013/2014

CM Chemical Spectroscopy and Applications. Final Examination Solution Manual AY2013/2014 NANYANG TECHNOLOGICAL UNIVERSITY DIVISION OF CHEMISTRY AND BIOLOGICAL CHEMISTRY SCHOOL OF PHYSICAL & MATHEMATICAL SCIENCES CM 3011 - Chemical Spectroscopy and Applications Final Examination Solution Manual

More information

Basic principles of multidimensional NMR in solution

Basic principles of multidimensional NMR in solution Basic principles of multidimensional NMR in solution 19.03.2008 The program 2/93 General aspects Basic principles Parameters in NMR spectroscopy Multidimensional NMR-spectroscopy Protein structures NMR-spectra

More information

NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala

NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala UCLEIC ACIDS Basic terms and notions Presentation by Eva Fadrná adapted by Radovan Fiala RA vs DA Single strand A-RA B-DA duplex Length of A Total length of DA in a human cell 1 m (1000 km) DA in typical

More information

Clickers. a. I watched all 5 videos b. The dog ate my iphone

Clickers. a. I watched all 5 videos b. The dog ate my iphone Clickers a. I watched all 5 videos b. The dog ate my iphone 40% 33% 33% 40% 59% 67% of you: Watch youtube! PRBLEMS: Complete end of chapter 13 problems 1 10 from Lab Manual Answers 1 NMR Protons (nucleus

More information

positive: correlation between H(1) and (2)

positive: correlation between H(1) and (2) 1 2 3 4 5 6 7 8 9-12 1D 1 H spectrum irradiated peak positive: correlation between H(1) and (2) positive and negative: H(1) and H(8) COSY 1D NOESY spectrum negative: exchange due to OH(7) 3.5 3.0 2.5 2.0

More information

Protein Structure Determination using NMR Spectroscopy. Cesar Trinidad

Protein Structure Determination using NMR Spectroscopy. Cesar Trinidad Protein Structure Determination using NMR Spectroscopy Cesar Trinidad Introduction Protein NMR Involves the analysis and calculation of data collected from multiple NMR techniques Utilizes Nuclear Magnetic

More information

Midterm Exam: CHEM/BCMB 8190 (148 points) Friday, 3 March, 2017

Midterm Exam: CHEM/BCMB 8190 (148 points) Friday, 3 March, 2017 Midterm Exam: CHEM/BCMB 8190 (148 points) Friday, 3 March, 2017 INSTRUCTIONS: You will have 50 minute to work on this exam. You can use any notes or books that you bring with you to assist you in answering

More information

Chem 213 Final 2012 Detailed Solution Key for Structures A H

Chem 213 Final 2012 Detailed Solution Key for Structures A H Chem 213 Final 2012 Detailed Solution Key for Structures A H COMPOUND A on Exam Version A (B on Exam Version B) C 8 H 6 Cl 2 O 2 DBE = 5 (aromatic + 1) IR: 1808 cm 1 suggests an acid chloride since we

More information

Supporting Information. Unique identifiers for small molecules enable rigorous labeling of their atoms

Supporting Information. Unique identifiers for small molecules enable rigorous labeling of their atoms Supporting Information Unique identifiers for small molecules enable rigorous labeling of their atoms Hesam Dashti, William M. Westler, John L. Markley, Hamid R. Eghbalnia National Magnetic Resonance Facility

More information

7 Infrared, Thermochemistry, UV-Vis, and NMR

7 Infrared, Thermochemistry, UV-Vis, and NMR 7 Infrared, Thermochemistry, UV-Vis, and NMR Exercise 1 Method Dependence and Scaling for the Infrared Spectrum of Formaldehyde. Build a molecule of formaldehyde using sp 2 C and atoms. Clean up the structure

More information

4. NMR spectra. Interpreting NMR spectra. Low-resolution NMR spectra. There are two kinds: Low-resolution NMR spectra. High-resolution NMR spectra

4. NMR spectra. Interpreting NMR spectra. Low-resolution NMR spectra. There are two kinds: Low-resolution NMR spectra. High-resolution NMR spectra 1 Interpreting NMR spectra There are two kinds: Low-resolution NMR spectra High-resolution NMR spectra In both cases the horizontal scale is labelled in terms of chemical shift, δ, and increases from right

More information

NMR Structure Determination of Saccharose and Raffinose by Means of Homo- and Heteronuclear Dipolar Couplings

NMR Structure Determination of Saccharose and Raffinose by Means of Homo- and Heteronuclear Dipolar Couplings Helvetica Chimica Acta ± Vol. 84 (2001) 243 NMR Structure Determination of Saccharose and Raffinose by Means of Homo- and Heteronuclear Dipolar Couplings by Heike Neubauer, Jens Meiler, Wolfgang Peti,

More information

Using NMR and IR Spectroscopy to Determine Structures Dr. Carl Hoeger, UCSD

Using NMR and IR Spectroscopy to Determine Structures Dr. Carl Hoeger, UCSD Using NMR and IR Spectroscopy to Determine Structures Dr. Carl Hoeger, UCSD The following guidelines should be helpful in assigning a structure from NMR (both PMR and CMR) and IR data. At the end of this

More information

Relaxation, Multi pulse Experiments and 2D NMR

Relaxation, Multi pulse Experiments and 2D NMR Relaxation, Multi pulse Experiments and 2D NMR To Do s Read Chapter 6 Complete the end of chapter problems; 6 1, 6 2, 6 3, 6 5, 6 9 and 6 10. Read Chapter 15 and do as many problems as you can. Relaxation

More information

Conformations of Flexible Oligosaccharides: Molecular Simulations and NMR Spectroscopy. Robert Pendrill

Conformations of Flexible Oligosaccharides: Molecular Simulations and NMR Spectroscopy. Robert Pendrill Conformations of Flexible ligosaccharides: Molecular Simulations and NMR Spectroscopy Robert Pendrill i Robert Pendrill, Stockholm 2013 Cover picture: Spectral densities. ISBN 978-91-7447-808-2 Printed

More information

7 Steroids and sugars

7 Steroids and sugars 7 Steroids and sugars Purpose In this chapter you widen your scope on stereochemistry from that of relatively simple compounds to that of more complex and naturally occurring compounds. ne stereochemically

More information

(J=11.4Hz, 1=4.7Hz) which were decoupled

(J=11.4Hz, 1=4.7Hz) which were decoupled VOL. XXIV NO. 1 TE JOURNAL OF ANTIBIOTICS 59 STUDIES ON VALIDAMYCINS, NEW ANTIBIOTICS. VI VALIDAMINE, YDROXYVALIDAMINE AND VALIDATOL, NEW CYCLITOLS Sir: four-carbon amino group sequence which has one primary

More information

NMR in Medicine and Biology

NMR in Medicine and Biology NMR in Medicine and Biology http://en.wikipedia.org/wiki/nmr_spectroscopy MRI- Magnetic Resonance Imaging (water) In-vivo spectroscopy (metabolites) Solid-state t NMR (large structures) t Solution NMR

More information

11/14/2016. NaBH 4. Superimposable on mirror image. (achiral) D-ribose. NaBH 4 NaBH 4. Not superimposable on mirror image.

11/14/2016. NaBH 4. Superimposable on mirror image. (achiral) D-ribose. NaBH 4 NaBH 4. Not superimposable on mirror image. There are multiple ways to relate the structures of ketoses to aldoses. Reduction of a ketose with NaB 4 forms a new stereocenter and thus forms a mixture of two alditols. An aldopentose forms a chiral

More information

CSIRO Land & Water, Black Mountain Science and Innovation Park, Acton, ACT 2601, Australia

CSIRO Land & Water, Black Mountain Science and Innovation Park, Acton, ACT 2601, Australia Isolation of the (+)-pinoresinol-mineralizing Pseudomonas sp. SG-MS2 and elucidation of its catabolic pathway Madhura Shettigar a,b, Sahil Balotra a, David Cahill b, Andrew C. Warden a, Michael J. Lacey

More information

Chapter 14. Nuclear Magnetic Resonance Spectroscopy

Chapter 14. Nuclear Magnetic Resonance Spectroscopy Organic Chemistry, Second Edition Janice Gorzynski Smith University of Hawai i Chapter 14 Nuclear Magnetic Resonance Spectroscopy Prepared by Rabi Ann Musah State University of New York at Albany Copyright

More information

Constitutional Isomers and Conformations of Alkanes & Cycloalkanes

Constitutional Isomers and Conformations of Alkanes & Cycloalkanes Discovering Molecular Models #1: Constitutional Isomers Conformations of Alkanes & Cycloalkanes There are no additional tutorial or laboratory notes. Read bring your course notes, as they provide all of

More information

NMR Resonance Assignment Assisted by Mass Spectrometry

NMR Resonance Assignment Assisted by Mass Spectrometry NMR Resonance Assignment Assisted by Mass Spectrometry This lecture talked about a NMR resonance assignment assisted by mass spectrometry [1, 2]. 1 Motivation Nuclear magnetic resonance (NMR) provides

More information

Constitutional Isomers and Conformations of Alkanes & Cycloalkanes

Constitutional Isomers and Conformations of Alkanes & Cycloalkanes Discovering Molecular Models #1: Constitutional Isomers Conformations of Alkanes & Cycloalkanes There are no additional tutorial or laboratory notes. Read bring your course notes, as they provide all of

More information

1. The barrier to rotation around the C-C bonds for 2-methylpropane and 2,2-dimethylpropane are shown below.

1. The barrier to rotation around the C-C bonds for 2-methylpropane and 2,2-dimethylpropane are shown below. 1. The barrier to rotation around the C-C bonds for 2-methylpropane and 2,2-dimethylpropane are shown below. E Rot = 14.2 kj/mol E Rot = 19.6 kj/mol a. Why does the potential energy of a molecule increase

More information

Computational Chemistry Lab Module: Conformational Analysis of Alkanes

Computational Chemistry Lab Module: Conformational Analysis of Alkanes Introduction Computational Chemistry Lab Module: Conformational Analysis of Alkanes In this experiment, we will use CAChe software package to model the conformations of butane, 2-methylbutane, and substituted

More information

Triple Resonance Experiments For Proteins

Triple Resonance Experiments For Proteins Triple Resonance Experiments For Proteins Limitations of homonuclear ( 1 H) experiments for proteins -the utility of homonuclear methods drops quickly with mass (~10 kda) -severe spectral degeneracy -decreased

More information

et[ailn B:ag;el Research Limited LIBRARY TECHNICAL FILES.

et[ailn B:ag;el Research Limited LIBRARY TECHNICAL FILES. ja 15 ' 76 et[ailn B:ag;el Research Limited LIBRARY TECHNICAL FILES.,...., rife -+ {-- *b A.- i a e; t V t~ AX ;, A, : d d-. *. -. -1s \ I '~:, - r... -_,-, -...-- _.---.A..h $ I. m THE INSTITUTE OF PAPER

More information

Common Multiplet Patterns and Their Analysis

Common Multiplet Patterns and Their Analysis Common Multiplet Patterns and Their Analysis AB and AX systems AX: Two protons, H A and H X, very different shifts. First order. J AX can be directly obtained. AB : Two protons, H A and H B, chemical shifts

More information

H B. θ = 90 o. Lecture notes Part 4: Spin-Spin Coupling. θ θ

H B. θ = 90 o. Lecture notes Part 4: Spin-Spin Coupling. θ θ Lecture notes Part 4: Spin-Spin Coupling F. olger Försterling October 4, 2011 So far, spins were regarded spins isolated from each other. owever, the magnetic moment of nuclear spins also have effect on

More information

Exam 1 Chem 3045x Friday, October 1, 1999 ANSWER KEY: Exam 1. C3043. Friday, October 1, 1999 p. 1

Exam 1 Chem 3045x Friday, October 1, 1999 ANSWER KEY: Exam 1. C3043. Friday, October 1, 1999 p. 1 Exam 1 Chem 3045x Friday, ctober 1, 1999 ANSWER KEY: Exam 1. C3043. Friday, ctober 1, 1999 p. 1 1. (10 Points). Consider the composition C 2 N 2. Draw the Lewis structures of 5 constitutional isomers which

More information

BMB/Bi/Ch 173 Winter 2018

BMB/Bi/Ch 173 Winter 2018 BMB/Bi/Ch 173 Winter 2018 Homework Set 8.1 (100 Points) Assigned 2-27-18, due 3-6-18 by 10:30 a.m. TA: Rachael Kuintzle. Office hours: SFL 220, Friday 3/2 4-5pm and SFL 229, Monday 3/5 4-5:30pm. 1. NMR

More information

J. Sauri, R.D. Cohen, Y. Liu, M. Reibarkh, A.V. Buevich, R.T. Williamson & G.E. Martin

J. Sauri, R.D. Cohen, Y. Liu, M. Reibarkh, A.V. Buevich, R.T. Williamson & G.E. Martin 1,1-ADEQUATE Exclusively Affords 1 J CC Correlations 1 Bruker NMR User s Meeting SMASH 2016 Well Most of the Time! J. Sauri, R.D. Cohen, Y. Liu, M. Reibarkh, A.V. Buevich, R.T. Williamson & G.E. Martin

More information

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2014 Dr. Rainer Glaser

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2014 Dr. Rainer Glaser Chemistry 2030 Survey of Organic Chemistry Fall Semester 2014 Dr. Rainer Glaser Examination #1 Bonding, Alkanes, Alkenes & Alkynes Thursday, September 18, 2014, 8:00 8:50 am Question 1. Atomic Structure

More information

Experimental Determination of Pseudorotation Potentials for Disubstituted Cyclopentanes Based on Spin Spin Coupling Constants

Experimental Determination of Pseudorotation Potentials for Disubstituted Cyclopentanes Based on Spin Spin Coupling Constants Int. J. Mol. Sci. 003, 4, 107-118 International Journal of Molecular Sciences ISSN 14-0067 003 by MDPI www.mdpi.org/ijms/ Experimental Determination of Pseudorotation Potentials for Disubstituted Cyclopentanes

More information

BMB/Bi/Ch 173 Winter 2018

BMB/Bi/Ch 173 Winter 2018 BMB/Bi/Ch 173 Winter 2018 Homework Set 8.1 (100 Points) Assigned 2-27-18, due 3-6-18 by 10:30 a.m. TA: Rachael Kuintzle. Office hours: SFL 220, Friday 3/2 4:00-5:00pm and SFL 229, Monday 3/5 4:00-5:30pm.

More information

Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850, United States

Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850, United States Electronic Supplementary Material (ESI) for Dalton Transactions. This journal is The Royal Society of Chemistry 2016 Analysis of the isomer ratios of polymethylated DOTA complexes and the implications

More information

NMR atructural analysis of a novel triterpenoid saponin extracted from Bellis perennis L.

NMR atructural analysis of a novel triterpenoid saponin extracted from Bellis perennis L. NMR atructural analysis of a novel triterpenoid saponin extracted from Bellis perennis L. Michal Štujber a, Didem Sohretoglu b, Tibor Liptaj a a Department of NMR Spectroscopy and Mass Spectrometry, Faculty

More information

EXAMINATION 1 Chemistry 3A

EXAMINATION 1 Chemistry 3A 1 EXAMINATION 1 Chemistry 3A Name: Key Print first name before second! Use capital letters! SID #: Peter Vollhardt February 18, 2016 GSI (if you are taking Chem 3AL): Please provide the following information

More information

STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES CONFORMATIONAL ISOMERS

STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES CONFORMATIONAL ISOMERS STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES CONFORMATIONAL ISOMERS 1 CONFORMATIONAL ISOMERS Stereochemistry concerned with the 3-D aspects of molecules Rotation is possible around C-C bonds in openchain

More information

Chem 1140; Molecular Modeling

Chem 1140; Molecular Modeling P. Wipf 1 Chem 1140 $E = -! (q a + q b )" ab S ab + ab!k

More information

PROTEIN NMR SPECTROSCOPY

PROTEIN NMR SPECTROSCOPY List of Figures List of Tables xvii xxvi 1. NMR SPECTROSCOPY 1 1.1 Introduction to NMR Spectroscopy 2 1.2 One Dimensional NMR Spectroscopy 3 1.2.1 Classical Description of NMR Spectroscopy 3 1.2.2 Nuclear

More information

Importance of Carbohydrates

Importance of Carbohydrates Chapter 25 Importance of Carbohydrates Distributed widely in nature Key intermediates of metabolism (sugars) Structural components of plants (cellulose) Central to materials of industrial products: paper,

More information

Chapter 1: NMR Coupling Constants

Chapter 1: NMR Coupling Constants NMR can be used for more than simply comparing a product to a literature spectrum. There is a great deal of information that can be learned from analysis of the coupling constants for a compound. 1.1 Coupling

More information

Chapter 3 AN INTRODUCTION TO ORGANIC COMPOUNDS NOMENCLATURE, PHYSICAL PROPERTIES, REPRESENTATION OF STRUCTURE AND

Chapter 3 AN INTRODUCTION TO ORGANIC COMPOUNDS NOMENCLATURE, PHYSICAL PROPERTIES, REPRESENTATION OF STRUCTURE AND ORGANIC CHEMISTRY, 2 ND EDITION PAULA YURKANIS BRUICE Chapter 3 AN INTRODUCTION TO ORGANIC COMPOUNDS NOMENCLATURE, PHYSICAL PROPERTIES, AND REPRESENTATION OF STRUCTURE RAED M. AL-ZOUBI, ASSISTANT PROFESSOR

More information

Two Dimensional (2D) NMR Spectroscopy

Two Dimensional (2D) NMR Spectroscopy The two important parameters obtained from NMR spectra are; Two Dimensional (2D) NMR Spectroscopy py Correlation NMR a. Chemical shift b. Spin-spin coupling constant Large molecules with numerous atoms

More information

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2017 Dr. Rainer Glaser

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2017 Dr. Rainer Glaser Chemistry 2030 Survey of Organic Chemistry Fall Semester 2017 Dr. Rainer Glaser Examination #1 Bonding, Alkanes, Alkenes & Alkynes Thursday, September 14, 2017, 8:25 9:15 am Name: Answer Key Question 1.

More information

Final Exam Chem 3045x Wednesday, Dec. 17, 1997

Final Exam Chem 3045x Wednesday, Dec. 17, 1997 Final Exam Chem 3045x Wednesday, Dec. 17, 1997 Instructions: This is a closed book examination. You may not use any notes, books or external materials during the course of the examination. Please print

More information

H-C one-bond correlations: HSQC Preliminaries.

H-C one-bond correlations: HSQC Preliminaries. A.- F. Miller 2010 C HSQC H-C one-bond correlations: HSQC Preliminaries. For both 1 H and C, you need a good power- pw90 pair and you should have good values for both sw and tof for both nuclei. In short,

More information

25.6 Cyclic Forms of Carbohydrates: Furanose Forms

25.6 Cyclic Forms of Carbohydrates: Furanose Forms .6 Cyclic Forms of Carbohydrates: Furanose Forms Recall from Section 7.8 R R' C + R" Product is a hemiacetal. R" C R R' R C Cyclic emiacetals R C Aldehydes and ketones that contain an group elsewhere in

More information

NMR NEWS October 2009

NMR NEWS October 2009 Department of Chemistry NMR Facilities Director: Dr. Carlos A. Steren NMR NEWS October 2009 To check on the instrumental status and reservation system, and find tutorials, links and more, visit our website

More information

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2015 Dr. Rainer Glaser

Chemistry 2030 Survey of Organic Chemistry Fall Semester 2015 Dr. Rainer Glaser Chemistry 2030 Survey of Organic Chemistry Fall Semester 2015 Dr. Rainer Glaser Examination #1 Bonding, Alkanes, Alkenes & Alkynes Thursday, September 17, 2015, 8:25 9:15 am Question 1. Atomic Structure,

More information

Molecular Modeling and Conformational Analysis with PC Spartan

Molecular Modeling and Conformational Analysis with PC Spartan Molecular Modeling and Conformational Analysis with PC Spartan Introduction Molecular modeling can be done in a variety of ways, from using simple hand-held models to doing sophisticated calculations on

More information

Collecting the data. A.- F. Miller 2012 DQF- COSY Demo 1

Collecting the data. A.- F. Miller 2012 DQF- COSY Demo 1 A.- F. Miller 2012 DQF- COSY Demo 1 gradient Double-Quantum-Filtered COSY (gdqf-cosy) This spectrum produces cross peaks exclusively between 1 Hs that are connected through bonds, usually 3 or less. (Exceptions

More information

Glucose Anomers. Conformational Analysis by NMR

Glucose Anomers. Conformational Analysis by NMR Glucose Anomers Conformational Analysis by NMR Glucose in solution remains mostly in the cyclic pyranose form in two conformational anomers shown in the figure above. These two forms interconvert via an

More information