Protein Dynamics by NMR. Why NMR is the best!
|
|
- Shawn Sanders
- 8 years ago
- Views:
Transcription
1 Protein Dynamics by NMR Why NMR is the best!
2 Key Points NMR dynamics divided into 2 regimes: fast and slow. How protein mobons affect NMR parameters depend on whether they are faster or slower than the rotabonal correlabon Bme Fast Bmescale dynamics (ps ns) limited by rotabonal correlabon Bme of protein parameters describe distribubon of states Slower Bmescale dynamics (µs ms) require chemical shil difference measured more directly
3 Protein Dynamics by NMR H N Relaxation T1, T2, heteronuclear NOE Relaxation T1ρ, CPMG Lineshape analysis ZZ-exchange, NOESY H/D exchange
4 NMR Timescales Transport, catalysis, many interesbng biological processes.. ps ns µs ms sec >hrs Relaxa&on T1, T2, HETNOE Relaxa>on T1ρ, CPMG Satura>on transfer ZZ exchange, NOESY Line shape analysis H/D exchange
5 Slow Timescale Exchange Great for characterizing a 2 state process: Open vs closed conformabon of a protein Free vs bound state Folded vs unfolded 3 or more state More challenging to analyze quanbtabvely Strength of NMR Simultaneously measure exchange rate (kinebcs) populabons (thermodynamics) chemical shils (structural informabon) Site specific resolubon. Is the process global or local? If global, all residues should have the same exchange rate and populabons **Fast and slow regimes within the slow >mescale limit!!!**
6 Characterizing a 2 state processes G (k AB ) G p A,ω A State A: Structural info embedded in chemical shil, ω A p B,ω B G (k BA ) State B: Structural info embedded in chemical shil, ω B k A AB B k BA k ex = k BA + k AB Thermo: G= RTlnK eq K eq =p B /p A KineBcs: k ex =k BA +k AB k AB =p A k ex p A +p B =1 p A >p B k BA >k AB
7 Basic NMR reminders Chemical shil depends on the environment of the nucleus Hydrogen bonding, secondary structure, ring currents, electrostabcs, side chain torsion angles, etc. Two different states have two different chemical shils Integrate to determine populabons Just like organic chemistry integrate peaks to see which correspond to 1,2, or 3 protons. If two peaks correspond to the same nucleus in two states, then the integrals give the relabve populabons If peaks are of similar width, can use peak height instead of volume. z (B o ) Net magnebc moment Precession at chemical shil frequency
8 Basic NMR reminders Chemical shil is a precession frequency. Serves as a reference point for measuring protein dynamics. Slow Bmescale dynamics are described as fast or slow depending on the relabve values of k ex and ω (chemical shil difference between the two states). To convert from ν in ppm to ν in Hz: use ν=γb o /2π (ν=ω/2π ) ppm is parts per million, so 1ppm=600Hz on a 600MHz spectrometer. z (B o ) Net magnebc moment Precession at chemical shil frequency
9 TheoreBcal NMR line shapes for fast k ex >> ν two site exchange k ex (s 1 ) k A AB B k BA k ex = k BA + k AB 200 slow k ex << ν 20 < 0.1 Remember: Chemical shil difference ( ν) is a frequency. Popula>on Palmer, et al, Methods in Enzymology, 2001
10 Lineshape Analysis Requires a BtraBon TheoreBcal equabons for lineshape (including peak width, intensity, separabon) Parameters: intrinsic relaxabon rates (R 2o ), exchange rate (k ex ), populabons (p A ), chemical shil difference ( ν) Change condibons so that the values of the parameters change in disbnct ways so they can be deconvoluted Fit the lineshape as a funcbon of BtraBon Adding ligand (free vs bound) Adding denaturant (folded vs unfolded) Changing ph (pka determinabon) Changing temperature (folding, conformabonal change, almost any process)
11 Fast Exchange k ex >> ν Observe a single peak at the weighted average posibon. What happens upon BtraBon? As populabon shils, peak posibons shils Ex. ShiLing 2 state equilibrium State A=free State B=bound State A=folded State B=unfolded State A=open conformabon State B=closed conformabon If 600 MHz spectrometer, Then ν=1200 Hz k ex?
12 Slow Exchange k ex << ν Peaks don t shil. What happens upon BtraBon of a 2 state system? As populabon shils, peaks corresponding to each state appear/ disappear Ex. ShiLing 2 state equilibrium State A=free State B=bound State A=folded State B=unfolded State A=open conformabon State B=closed conformabon If 600 MHz spectrometer, Then ν=1200 Hz k ex?
13 OLen somewhere in the middle k ex and ω both influence the peak posibon/lineshape. Careful analysis can determine p A, k ex, and ω. ω will not be the same for all residues in a protein might have some in slow exchange, some in fast exchange, some in intermediate. Wolf Watz, et al. Nat. Struct. Mol. Biol. 11, a 4.0 mm 1.4 mm 0.8 mm 0 mm H (p.p.m) N (p.p.m) TitraBon of ligand (concentrabon indicated) into protein. A) shows a peak from the protein HSQC undergoing the transibon from free to bound. B) shows the 1D lineshape simulabon of the spectrum. b N (p.p.m)
14 Hidden exchange Skewed populabons what if you can t see the second state because it s only 2% populated? ex. Slow exchange but second peak so much less intense it s not observable) What if you can t Btrate something to reveal the exchange, but suspect that your protein is undergoing exchange? Or you want to quanbfy the exchange? Fast exchange: only see an average peak. Do you have a single state or is there an equilibrium? Slow exchange: 2 sets of peaks. Is it slow exchange or no exchange? NOESY, ZZ exchange helpful for ms s exchange (ms s) CPMG helpful for µs ms exchange
15 NOESY/ZZ analysis Basic strategy: Record inibal chemical shil, wait (mixing Bme), record final chemical shil No exchange: inibal and final states are the same (ω 1 =ω 2 ) observe diagonal/auto peak With exchange: chemical shil of final state is different than the inibal state observe crosspeak (ω 1 ω 2 ) NOTE: chemical shil of the two states must be different in order to observe the exchange Ex. regions close to binding interface will show the effect of binding, regions far away will not. By chance, even if there is a conformabonal change, an individual residue within that region may have the same chemical shil in both states. Useful for Slow exchange, 2sets of peaks already visible in spectrum Exchange rates 10s 100s of milliseconds Direct kinebc measurement vary mixing Bme and see how much conformabonal change occurs
16 NOESY Analysis 1 H Encode chemical shil (ω1) Mixing Bme Acquire data (chemical shil, ω2) Crosspeaks arise when: H B H B N 2 protons are close in space ω1 (ppm) H A H C2 H C1 State 1 State 2 H C1 H C2 ω2 (ppm) H A H B Slow conformabonal exchange between 2 states with different chemical shils
17 ZZ exchange Insert mixing >me (spins along z, hence the name ZZ exchange) Transfer magnebzabon from 1H to 15N Transfer magnebzabon from 15N to 1H HSQC Record chemical shil in indirect dimension (t 1 ), 15 N frequency in this case Record chemical shil in directly detected dimension (t 2 ), 1 H frequency in this case HSQC 15 N HSQC+ ZZ 15 N 2A 2B 1B (If no exchange, no addifonal peaks will be observed) 1A 1 H 1 H
18 NOESY/ZZ analysis Record ω 1, mixing Bme, record ω 2 Vary mixing Bme (10s 100s of milliseconds) Monitor build up of cross peaks and decay of auto peaks to determine exchange rate Since it s slow exchange da dt = R A 1 A k AB A + k BA B db dt = R B 1 B k BA B + k AB A R 1 is intrinsic relaxabon rate, k ex =k AB +k BA get populabons from relabve heights/volumes of inibal peaks Get chemical shil of inibal states from inibal peaks
19 ZZ exchange example N (ppm) In this example, the two peaks corresponding to a single amide in the HSQC have equal volumes, thus the two states are equally populated H (ppm)
20 ZZ exchange example da dt = R A 1 A k AB A + k BA B db dt = R B 1 B k BA B + k AB A Equal populabons means: da dt db = R A 1 k k k R B 1 k dt [ A] B
21 Characterizing a 2 state processes G (k AB )= G (k BA ) Thermo: G= RTlnK eq =0 K eq =p B /p A =1 G=0 p A,ω A p B,ω B State A: Structural info embedded in chemical shil, ω A State B: Structural info embedded in chemical shil, ω B KineBcs: k ex =k BA +k AB k AB =p A k ex p A +p B =1 p A =p B =0.5 k BA =k AB k AB A B k BA k BA = k AB
22 CPMG: Transverse RelaxaBon & ConformaBonal Exchange z z z 90 y T 2 delay B 0 x B 1 on x B 1 off x ω A y y y Chemical shil evolubon
23 CPMG z z z 90 y T 2 delay B 0 y x B 1 on y x B 1 off y x ω A Chemical shil evolubon + transverse relaxabon ω A Intrinsic linewidth R 2 0
24 CPMG z z z 90 y T 2 delay B 0 x B 1 on x B 1 off x ω A y y y ω B (Ignoring transverse relaxabon) 180 x z z x T 2 delay B 1 off ω B ω A x y No exchange, spins refocused, same linewidth. y
25 CPMG z z z B 0 y k AB A B k BA k BA = k AB exchange contributes to line broadening x 90 y B 1 on y y z addibonal dephasing x x T 2 delay B 1 off T 2 delay B 1 off y y z ω B 180 x x ω A AND exchange ω A ω B x Note: need a chemical shil difference!
26 CPMG: Transverse RelaxaBon & ConformaBonal Exchange R 2 (ν CPMG ) = R (p A p B ω 2 /k ex )(1 (4ν CPMG /k ex )tanh(k ex /4ν CPMG )) R 2 eff (Hz) R ex k ex =1660 s 1 ν CPMG (Hz) R 20 R ex = p A p B ω 2 /k ex What would a residue with no exchange look like? Relate ω to known chemical shil differences to assign exchanging states Use different field strength data to separate p A and ω. More frequent 180 pulses
27 CPMG example: Lid mobon is the rate limibng step in Adk catalysis T = 20 C mesoadk k close 1380 s 1 k open 282 s 1 k cat = 261 s 1 k cat Note the power of NMR: we can easily see that this is a global conformabonal exchange process. Residues all across the protein report the same populabons and exchange rate. Not all remote residues sense the change ( ω too small). Wolf Watz, et al. Nat. Struct. Mol. Biol. 11,
28 CPMG Notes Can see invisible states Detect presence of a second state by its effect on the linewidth of the first state. For slower exchange rates, can detect low populabons where signal isn t strong enough to observe directly. For faster exchange rates, can detect that a single peak actually reflects a populabon weighted average of exchanging states, not a single state. Can detect minor species with popula>ons as low as 0.5% Can reconstruct structures of these minor states Measure chemical shil difference, know chemical shil of major state, can calculate chemical shil of minor state. This predicts secondary structure of minor state Can also detect RDC of minor state and use that to orient structure elements. Can determine structure of a state that is too lowly populated for direct structure determinabon or is only transiently populated! (ex. Folding intermediates)
29 NtrC: ParBally AcBve Mutants Gardino, et al, Methods Enzymology (2007) 423: The NMR structures of NtrCr (blue) and P NtrCr (orange) are superimposed. PhosphorylaBon causes a conformabonal change from the inacbve (blue) to the acbve (orange) state.
30 NtrC: ParBally AcBve Mutants Gardino, et al, Methods Enzymology (2007) 423: Two state model for NtrC. WT More acbve mutants k ex >10000 Hz, fast exchange unphosphorylated I A 85% ParBally acbve mutant, unphosphorylated P NtrC I A Changes in peak posibon are shown for the backbone amide of D88. The pa~ern reflects the equilibrium between the two states. More acbve mutants have a higher percentage in the acbve conformabon, even in the absence of phosphorylabon. Phosphorylated I A 99% Note: ω values indicate the unphosphorylated and phosphorylated states are not the endpoints. Exchange is detectable in both phosphorylated and unphosphorylated states. Phosphoryla>on is not a perfect on/off switch!
31 Fast Timescale Dynamics Less intuibve than slow Bmescale dynamics Measure ps ns mobons Faster fluctuabons Small mobons Large number of states Reflect entropy of system, although exact calculabon is not parbcularly helpful Reflects re orientabonal mobon only, not affected by mobons along an internuclear vector Only observing a small subset of protein nuclei Ignores rest of protein, water, etc
32 Fast Timescale Dynamics Measure R 1, R 2, and heternuclear NOE Molecular tumbling (global) and protein mobon (local) cause fluctuabons in local magnebc field that lead to relaxabon. CorrelaBon between macroscopic relaxabon and microscopic fluctuabons follows the fluctuabon dissipabon theorem. Anisotropic interacbons (chemical shil anisotropy and dipolar coupling) depend on orientabon of molecule in magnebc field. As the protein moves, the local field due to these interacbons fluctuates, this causes loss of coherence (T2 relaxabon) and return to equilibrium (T1 relaxabon). SomeBmes the field has the right frequency to cause spin flips. This leads to NOE. RelaxaBon depends on the spectral density, J(ω) the probability of field fluctuabons of each frequency/energy within the thermal fluctuabons of the molecue. Only certain frequencies cause energy transfer between spins or between spins and la ce
33 Spectral Density Grzesiek, EMBO course 2007
34 Fast Timescale Dynamics Measure R 1, R 2, and heternuclear NOE Molecular tumbling (global) and protein mobon (local) cause fluctuabons in local magnebc field that lead to relaxabon. Model free analysis leads to fi ng of several parameters (per residue) as well as parameters describing overall tumbling of the molecule: S 2, order parameter, correla>on func>on at infinite >me Most robust, well determined. Ranges from 0 1 0=0 probability that you will sbll be in the same orientabon. Isotropic mobon 1=completely rigid. You will sbll be in the same orientabon at any Bme High (0.85) in secondary structure. Low ( ) in unstructured regions or intrinsically disordered proteins. τ, internal correlabon Bme, not very accurate. Only sensi&ve to local mo&on faster than global tumbling
35 Fast Bmescale dynamics τ c T1 T2 B o H N S 2, τ e NOE N H S Increasing flexibility S
36 Fast Timescale Dynamics Order parameters reflect fast Bmescale, small amplitude bond fluctuabons Can calculate from MD trajectories Higher order parameters in regions of secondary structure Reflect local packing can calculate order parameters reasonably well just by looking at local packing (# interacbons around a given residue) Reasonable agreement with B factors from crystal structure, if regions affected by crystal packing between molecules are avoided. S Residue 200
Lecture #7 (2D NMR) Utility of Resonance Assignments
Lecture #7 (2D NMR) Basics of multidimensional NMR (2D NMR) 2D NOESY, COSY and TOCSY 2/23/15 Utility of Resonance Assignments Resonance Assignments: Assignment of frequency positions of resonances (peaks)
More informationNMR for Physical and Biological Scientists Thomas C. Pochapsky and Susan Sondej Pochapsky Table of Contents
Preface Symbols and fundamental constants 1. What is spectroscopy? A semiclassical description of spectroscopy Damped harmonics Quantum oscillators The spectroscopic experiment Ensembles and coherence
More informationSpin-Lattice Relaxation Times
Spin-Lattice Relaxation Times Reading Assignment: T. D. W. Claridge, High Resolution NMR Techniques in Organic Chemistry, Chapter 2; E. Breitmaier, W. Voelter, Carbon 13 NMR Spectroscopy,3rd Ed., 3.3.2.
More informationVTT TECHNICAL RESEARCH CENTRE OF FINLAND
Figure from: http://www.embl.de/nmr/sattler/teaching Why NMR (instead of X ray crystallography) a great number of macromolecules won't crystallize) natural environmant (water) ligand binding and inter
More information8.1 Relaxation in NMR Spectroscopy
8.1 Relaxation in NMR Spectroscopy Copyright ans J. Reich 2010 All Rights Reserved University of Wisconsin An understanding of relaxation processes is important for the proper measurement and interpretation
More informationHow To Understand The Measurement Process
April 24, 2015 Exam #3: Solution Key online now! Graded exams by Monday! Final Exam Monday, May 4 th, 10:30 a.m. Room: Perkins 107 1 A Classical Perspective A classical view will help us understand the
More informationNMR Nuclear Magnetic Resonance
NMR Nuclear Magnetic Resonance Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. This energy is at a specific resonance
More informationBasic Principles of Magnetic Resonance
Basic Principles of Magnetic Resonance Contents: Jorge Jovicich jovicich@mit.edu I) Historical Background II) An MR experiment - Overview - Can we scan the subject? - The subject goes into the magnet -
More informationNMR practice times. Mo 2---8 pm Jim 2-4:30 Ning 4:30-7. Tues 2--- 8 pm Jianing 2-4:30 Ting 4:30-7. Fri 10- --- 7 Donia 10-12:00 Ilya 2-4
NMR practice times 1 Mo 2---8 pm Jim 2-4:30 Ning 4:30-7 Tues 2--- 8 pm Jianing 2-4:30 Ting 4:30-7 Wed 4:30---8 John 5:00-7:30 Fri 10- --- 7 Donia 10-12:00 Ilya 2-4 Samples are listed in the homework along
More informationNMR Spectroscopy in Notre Dame
NMR Spectroscopy in Notre Dame University of Notre Dame College of Science Department of Chemistry and Biochemistry Nuclear Magnetic Resonance Facility http://www.nd.edu/~nmr Reservation system for spectrometers
More informationElectronic Supplementary Information
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2016 Electronic Supplementary Information Achieving High Resolution and Controlling
More informationGE Medical Systems Training in Partnership. Module 8: IQ: Acquisition Time
Module 8: IQ: Acquisition Time IQ : Acquisition Time Objectives...Describe types of data acquisition modes....compute acquisition times for 2D and 3D scans. 2D Acquisitions The 2D mode acquires and reconstructs
More informationChemical Exchange in NMR Spectroscopy
COURSE#1022: Biochemical Applications of NMR Spectroscopy http://www.bioc.aecom.yu.edu/labs/girvlab/nmr/course/ Chemical Exchange in NMR Spectroscopy LAST UPDATE: 3/28/2012 1 References Bain, A. D. (2003).
More informationProtein Dynamics Intro
Protein Dynamics Intro From rigid structures to motions on energy landscapes Do you all remember Anfinsen? What concept now associated with his name made Anfinsen famous? Right, it is the concept that
More informationNMR SPECTROSCOPY. Basic Principles, Concepts, and Applications in Chemistry. Harald Günther University of Siegen, Siegen, Germany.
NMR SPECTROSCOPY Basic Principles, Concepts, and Applications in Chemistry Harald Günther University of Siegen, Siegen, Germany Second Edition Translated by Harald Günther JOHN WILEY & SONS Chichester
More informationChapter 1. Fundamentals of NMR THOMAS L. JAMES. Department of Pharmaceutical Chemistry University of California San Francisco, CA 94143-0446 U.S.A.
Chapter 1 Fundamentals of NMR THOMAS L. JAMES Department of Pharmaceutical Chemistry University of California San Francisco, CA 94143-0446 U.S.A. 1.1 INTRODUCTION 1.2 MAGNETIC RESONANCE Nuclear Spins The
More informationHow To Understand The Theory Of Quantum Theory
-- Notes on relaxation and dynamics EMBO Practical Course on NMR, Heidelberg, September 0-7, 003 Stephan Grzesiek Biozentrum der Universität Basel Klingelbergstr 70 CH-4056 Basel, Switzerland e-mail: stephan.grzesiek@unibas.ch.
More informationSignal Manipulation. time domain NMR signal in MHz range is converted to khz (audio) range by mixing with the reference ( carrier ) frequency
NMR Spectroscopy: 3 Signal Manipulation time domain NMR signal in MHz range is converted to khz (audio) range by mixing with the reference ( carrier ) frequency Ref in (MHz) mixer Signal in (MHz) Signal
More informationStructural Bioinformatics (C3210) Experimental Methods for Macromolecular Structure Determination
Structural Bioinformatics (C3210) Experimental Methods for Macromolecular Structure Determination Introduction Knowing the exact 3D-structure of bio-molecules is essential for any attempt to understand
More informationProton Nuclear Magnetic Resonance ( 1 H-NMR) Spectroscopy
Proton Nuclear Magnetic Resonance ( 1 H-NMR) Spectroscopy Theory behind NMR: In the late 1940 s, physical chemists originally developed NMR spectroscopy to study different properties of atomic nuclei,
More informationSpin-lattice and spin-spin relaxation
Spin-lattice and spin-spin relaation Sequence of events in the NMR eperiment: (i) application of a 90 pulse alters the population ratios, and creates transverse magnetic field components (M () ); (ii)
More informationINTRODUCTION TO CHEMICAL EXCHANGE WITH THE MEXICO PROGRAM
ITRODUCTIO TO CEMICAL EXCAGE WIT TE MEXICO PROGRAM TE PEOMEO May, 2001 C 3 C 3 C 3 C 3 C 3 C 3 Figure 1 Consider the molecule in figure 1: 3-dimethylamino-7-methyl-1,2,4- benzotriazine. As it is drawn,
More informationIntroduction to NMR spectroscopy. Swiss Institute of Bioinformatics I.Phan & J. Kopp
Introduction to NMR spectroscopy Swiss Institute of Bioinformatics I.Phan & J. Kopp NMR: the background Complex technique. Requires knowledge in: Mathematics Physics Chemistry Biology (Medicin) Involves
More informationThe Experiment Some nuclei have nuclear magnetic moments; just as importantly, some do not
Chemistry 2600 Lecture Notes Chapter 15 Nuclear Magnetic Resonance Spectroscopy Page 1 of 23 Structure Determination in Organic Chemistry: NMR Spectroscopy Three main techniques are used to determine the
More informationNuclear Magnetic Resonance (NMR) Spectroscopy
April 28, 2016 Exam #3: Graded exams on Tuesday! Final Exam Tuesday, May 10 th, 10:30 a.m. Room: Votey 207 (tentative) Review Session: Sunday, May 8 th, 4 pm, Kalkin 325 (tentative) Office Hours Next week:
More informationTable of contents. Bibliografische Informationen http://d-nb.info/1006571213. digitalisiert durch
1. Research scope: The role of structure rigid'tf'ication in nature and chemistry 1 2. Establishing a Dha=Tap backbone scan in order to elucidate structural properties of the N-terminusofNPY 5 2.1 Introduction.
More information13C NMR Spectroscopy
13 C NMR Spectroscopy Introduction Nuclear magnetic resonance spectroscopy (NMR) is the most powerful tool available for structural determination. A nucleus with an odd number of protons, an odd number
More informationReview of Chemical Equilibrium 7.51 September 1999. free [A] (µm)
Review of Chemical Equilibrium 7.51 September 1999 Equilibrium experiments study how the concentration of reaction products change as a function of reactant concentrations and/or reaction conditions. For
More informationNMR Pulse Spectrometer PS 15. experimental manual
NMR Pulse Spectrometer PS 15 experimental manual NMR Pulse Spectrometer PS 15 Experimental Manual for MS Windows For: MS Windows software Winner Format: MS Word 2002 File: PS15 Experimental Manual 1.5.1.doc
More informationBUILDING BLOCKS FOR MULTIDIMENSIONAL NMR AND SPECIAL CONSIDERATIONS FOR BIOLOGICAL APPLICATIONS OF NMR
09-Pochapsky-09-cpp 3/7/06 2:9 pm Page 24 9 BUILDING BLOCKS FOR MULTIDIMENSIONAL NMR AND SPECIAL CONSIDERATIONS FOR BIOLOGICAL APPLICATIONS OF NMR The development of multidimensional NMR (three or more
More informationNuclear Magnetic Resonance Spectroscopy
Nuclear Magnetic Resonance Spectroscopy Nuclear magnetic resonance spectroscopy is a powerful analytical technique used to characterize organic molecules by identifying carbonhydrogen frameworks within
More informationNuclear Magnetic Resonance Spectroscopy
Nuclear Magnetic Resonance Spectroscopy Introduction NMR is the most powerful tool available for organic structure determination. It is used to study a wide variety of nuclei: 1 H 13 C 15 N 19 F 31 P 2
More informationTopic 2: Energy in Biological Systems
Topic 2: Energy in Biological Systems Outline: Types of energy inside cells Heat & Free Energy Energy and Equilibrium An Introduction to Entropy Types of energy in cells and the cost to build the parts
More informationHYDRONMR and Fast-HYDRONMR
File:hydronmr7c-pub.doc HYDRONMR and Fast-HYDRONMR Index 1. Introduction to HYDRONMR 2. Literature 3. Running HYDRONMR. Input data file 4. Output files 5. Notes and hints 7. Release notes Version 7c, September
More informationProton Nuclear Magnetic Resonance Spectroscopy
CHEM 334L Organic Chemistry Laboratory Revision 2.0 Proton Nuclear Magnetic Resonance Spectroscopy In this laboratory exercise we will learn how to use the Chemistry Department's Nuclear Magnetic Resonance
More informationPROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (H-NMR)
PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (H-NMR) WHAT IS H-NMR SPECTROSCOPY? References: Bruice 14.1, 14.2 Introduction NMR or nuclear magnetic resonance spectroscopy is a technique used to determine
More informationGeneration and Detection of NMR Signals
Generation and Detection of NMR Signals Hanudatta S. Atreya NMR Research Centre Indian Institute of Science NMR Spectroscopy Spin (I)=1/2h B 0 Energy 0 = B 0 Classical picture (B 0 ) Quantum Mechanical
More informationOrganic Chemistry Tenth Edition
Organic Chemistry Tenth Edition T. W. Graham Solomons Craig B. Fryhle Welcome to CHM 22 Organic Chemisty II Chapters 2 (IR), 9, 3-20. Chapter 2 and Chapter 9 Spectroscopy (interaction of molecule with
More informationConcept 2. A. Description of light-matter interaction B. Quantitatities in spectroscopy
Concept 2 A. Description of light-matter interaction B. Quantitatities in spectroscopy Dipole approximation Rabi oscillations Einstein kinetics in two-level system B. Absorption: quantitative description
More informationWhat is molecular dynamics (MD) simulation and how does it work?
What is molecular dynamics (MD) simulation and how does it work? A lecture for CHM425/525 Fall 2011 The underlying physical laws necessary for the mathematical theory of a large part of physics and the
More information4. It is possible to excite, or flip the nuclear magnetic vector from the α-state to the β-state by bridging the energy gap between the two. This is a
BASIC PRINCIPLES INTRODUCTION TO NUCLEAR MAGNETIC RESONANCE (NMR) 1. The nuclei of certain atoms with odd atomic number, and/or odd mass behave as spinning charges. The nucleus is the center of positive
More informationAdvanced Physics Labs SEPT 2006. Pulsed NMR
Advanced Physics Labs SEP006 Pulsed NMR Pulsed NMR is widely used for chemical analysis, in Magnetic Resonance Imaging (MRI), and a number of other applications of magnetic resonance. In this lab you will
More informationThe Hydrogen Atom Is a Magnet. http://www.seed.slb.com/en/scictr/watch/gashydrates/detecting.htm
The Hydrogen Atom Is a Magnet Nuclear Magnetic Resonance Spectroscopy (NMR) Proton NMR A hydrogen nucleus can be viewed as a proton, which can be viewed as a spinning charge. As with any spinning charge,
More informationNatively Disordered Proteins
Natively Disordered Proteins 1 Gary W. Daughdrill, 2 Gary J. Pielak, 3 Vladimir N. Uversky, 4 Marc S. Cortese, and 4 A. Keith Dunker 1 Department of Microbiology, Molecular Biology, and Biochemistry, University
More informationProton Nuclear Magnetic Resonance Spectroscopy
Proton Nuclear Magnetic Resonance Spectroscopy Introduction: The NMR Spectrum serves as a great resource in determining the structure of an organic compound by revealing the hydrogen and carbon skeleton.
More informationProton NMR. One Dimensional H-NMR. Cl S. Common types of NMR experiments: 1-H NMR
Common types of NMR experiments: 1- NMR Proton NMR ne Dimensional -NMR a. Experiment igh field proton NMR (400Mz). single-pulse experiment. b. Spectral nterpretation i. Number of multiplets gives the different
More informationNMR Signal Properties & Data Processing
COURSE#1022: Biochemical Applications of NMR Spectroscopy http://www.bioc.aecom.yu.edu/labs/girvlab/nmr/course/ NMR Signal Properties & Data Processing LAST UPDATE: 1/13/2012 Reading Selected Readings
More informationUsed to determine relative location of atoms within a molecule Most helpful spectroscopic technique in organic chemistry Related to MRI in medicine
Structure Determination: Nuclear Magnetic Resonance CHEM 241 UNIT 5C 1 The Use of NMR Spectroscopy Used to determine relative location of atoms within a molecule Most helpful spectroscopic technique in
More informationQuantum control of individual electron and nuclear spins in diamond lattice
Quantum control of individual electron and nuclear spins in diamond lattice Mikhail Lukin Physics Department, Harvard University Collaborators: L.Childress, M.Gurudev Dutt, J.Taylor, D.Chang, L.Jiang,A.Zibrov
More informationNMR Techniques Applied to Mineral Oil, Water, and Ethanol
NMR Techniques Applied to Mineral Oil, Water, and Ethanol L. Bianchini and L. Coffey Physics Department, Brandeis University, MA, 02453 (Dated: February 24, 2010) Using a TeachSpin PS1-A pulsed NMR device,
More informationThe accurate calibration of all detectors is crucial for the subsequent data
Chapter 4 Calibration The accurate calibration of all detectors is crucial for the subsequent data analysis. The stability of the gain and offset for energy and time calibration of all detectors involved
More informationExamination of Proton NMR Spectra
Examination of Proton NMR Spectra What to Look For 1) Number of Signals --- indicates how many "different kinds" of protons are present. 2) Positions of the Signals --- indicates something about magnetic
More informationPractical guide for quantitative 1D NMR integration Eugenio Alvarado, University of Michigan, 05/10/10
Practical guide for quantitative 1D NMR integration Eugenio Alvarado, University of Michigan, 05/10/10 The purpose of this manuscript is not to present a discussion about quantitative NMR, but to offer
More informationANALYZER BASICS WHAT IS AN FFT SPECTRUM ANALYZER? 2-1
WHAT IS AN FFT SPECTRUM ANALYZER? ANALYZER BASICS The SR760 FFT Spectrum Analyzer takes a time varying input signal, like you would see on an oscilloscope trace, and computes its frequency spectrum. Fourier's
More informationNMR-the basic principles and its use in studies of water/ethanol/mixture
NMR-the basic principles and its use in studies of water/ethanol/mixture Ayhan DEMİR, Bachelor Degree Project in Chemistry, 15 ECTS, April 2012, Sweden. Supervisor: Prof. Per Olof WESTLUND, Dr.Tobias SPARRMAN
More informationMolecular Spectroscopy
Molecular Spectroscopy UV-Vis Spectroscopy Absorption Characteristics of Some Common Chromophores UV-Vis Spectroscopy Absorption Characteristics of Aromatic Compounds UV-Vis Spectroscopy Effect of extended
More informationBackground A nucleus with an odd atomic number or an odd mass number has a nuclear spin that can be observed by NMR spectrometers.
NMR Spectroscopy I Reading: Wade chapter, sections -- -7 Study Problems: -, -7 Key oncepts and Skills: Given an structure, determine which protons are equivalent and which are nonequivalent, predict the
More informationStructure Determination
5 Structure Determination Most of the protein structures described and discussed in this book have been determined either by X-ray crystallography or by nuclear magnetic resonance (NMR) spectroscopy. Although
More informationIndiana's Academic Standards 2010 ICP Indiana's Academic Standards 2016 ICP. map) that describe the relationship acceleration, velocity and distance.
.1.1 Measure the motion of objects to understand.1.1 Develop graphical, the relationships among distance, velocity and mathematical, and pictorial acceleration. Develop deeper understanding through representations
More informationTetramethylsilane (TMS) Trimethylsilyl d 4. -propionic acid (TMSP) Dioxane. O - Na + Dimethylfura n. Potassium Hydrogen Phthalate. Sodium Maleate CH 3
Practical Aspects of Quantitative NMR Experiments This discussion presumes that you already have an understanding of the basic theory of NMR. There are a number of issues that should be considered when
More informationPulsed Fourier Transform NMR The rotating frame of reference. The NMR Experiment. The Rotating Frame of Reference.
Pulsed Fourier Transform NR The rotating frame of reference The NR Eperiment. The Rotating Frame of Reference. When we perform a NR eperiment we disturb the equilibrium state of the sstem and then monitor
More information7. DYNAMIC LIGHT SCATTERING 7.1 First order temporal autocorrelation function.
7. DYNAMIC LIGHT SCATTERING 7. First order temporal autocorrelation function. Dynamic light scattering (DLS) studies the properties of inhomogeneous and dynamic media. A generic situation is illustrated
More informationTime out states and transitions
Time out states and transitions Spectroscopy transitions between energy states of a molecule excited by absorption or emission of a photon hn = DE = E i - E f Energy levels due to interactions between
More informationLecture 15: Enzymes & Kinetics Mechanisms
ROLE OF THE TRANSITION STATE Lecture 15: Enzymes & Kinetics Mechanisms Consider the reaction: H-O-H + Cl - H-O δ- H Cl δ- HO - + H-Cl Reactants Transition state Products Margaret A. Daugherty Fall 2004
More informationNMR - Basic principles
NMR - Basic principles Subatomic particles like electrons, protons and neutrons are associated with spin - a fundamental property like charge or mass. In the case of nuclei with even number of protons
More informationHow To Understand The Physics Of Ft Nmr
Basic Practical NMR Concepts: A Guide for the Modern Laboratory Description: This handout is designed to furnish you with a basic understanding of Nuclear Magnetic Resonance (NMR) Spectroscopy as it pertains
More informationProtein Studies Using CAChe
Protein Studies Using CAChe Exercise 1 Building the Molecules of Interest, and Using the Protein Data Bank In the CAChe workspace, click File / pen, and navigate to the C:\Program Files\Fujitsu\ CAChe\Fragment
More informationEnergy & Enzymes. Life requires energy for maintenance of order, growth, and reproduction. The energy living things use is chemical energy.
Energy & Enzymes Life requires energy for maintenance of order, growth, and reproduction. The energy living things use is chemical energy. 1 Energy exists in two forms - potential and kinetic. Potential
More informationNMR and other Instrumental Techniques in Chemistry and the proposed National Curriculum.
NMR and other Instrumental Techniques in Chemistry and the proposed National Curriculum. Dr. John Jackowski Chair of Science, Head of Chemistry Scotch College Melbourne john.jackowski@scotch.vic.edu.au
More informationCHAPTER 6 AN INTRODUCTION TO METABOLISM. Section B: Enzymes
CHAPTER 6 AN INTRODUCTION TO METABOLISM Section B: Enzymes 1. Enzymes speed up metabolic reactions by lowering energy barriers 2. Enzymes are substrate specific 3. The active site in an enzyme s catalytic
More information1 The water molecule and hydrogen bonds in water
The Physics and Chemistry of Water 1 The water molecule and hydrogen bonds in water Stoichiometric composition H 2 O the average lifetime of a molecule is 1 ms due to proton exchange (catalysed by acids
More informationMRI SEQUENCES. 1 Gradient Echo Sequence
5 An MRI sequence is an ordered combination of RF and gradient pulses designed to acquire the data to form the image. In this chapter I will describe the basic gradient echo, spin echo and inversion recovery
More informationDetermination of Equilibrium Constants using NMR Spectrscopy
CHEM 331L Physical Chemistry Laboratory Revision 1.0 Determination of Equilibrium Constants using NMR Spectrscopy In this laboratory exercise we will measure a chemical equilibrium constant using key proton
More informationMassachusetts Institute of Technology Department of Chemistry 5.33 Advanced Chemical Instrumentation FALL SEMESTER 2005
Massachusetts Institute of Technology Department of Chemistry 5.33 Advanced Chemical Instrumentation FALL SEMESTER 2005 EXPERIMENT #2A: MAGNETIC RESONANCE SPECTROSCOPY I. Introduction Magnetic resonance
More informationAPSYN420A/B Specification 1.24. 0.65-20.0 GHz Low Phase Noise Synthesizer
APSYN420A/B Specification 1.24 0.65-20.0 GHz Low Phase Noise Synthesizer 1 Introduction The APSYN420 is a wideband low phase-noise synthesizer operating from 0.65 to 20 GHz. The nominal output power is
More information7 Two-dimensional NMR
7 Two-dimensional NMR 7. Introduction The basic ideas of two-dimensional NMR will be introduced by reference to the appearance of a COSY spectrum; later in this chapter the product operator formalism will
More informationEnergy comes in many flavors!
Forms of Energy Energy is Fun! Energy comes in many flavors! Kinetic Energy Potential Energy Thermal/heat Energy Chemical Energy Electrical Energy Electrochemical Energy Electromagnetic Radiation Energy
More information1. Free energy with controlled uncertainty 2. The modes of ligand binding to DNA
1. Free energy with controlled uncertainty 2. The modes of ligand binding to DNA Tomáš Kubař Institute of Organic Chemistry and Biochemistry Praha, Czech Republic Thermodynamic Integration Alchemical change
More informationNMR and IR spectra & vibrational analysis
Lab 5: NMR and IR spectra & vibrational analysis A brief theoretical background 1 Some of the available chemical quantum methods for calculating NMR chemical shifts are based on the Hartree-Fock self-consistent
More informationNuclear Magnetic Resonance
Nuclear Magnetic Resonance Author: James Dragan Lab Partner: Stefan Evans Physics Department, Stony Brook University, Stony Brook, NY 794. (Dated: December 5, 23) We study the principles behind Nuclear
More information1 The basic equations of fluid dynamics
1 The basic equations of fluid dynamics The main task in fluid dynamics is to find the velocity field describing the flow in a given domain. To do this, one uses the basic equations of fluid flow, which
More informationNuclear Magnetic Resonance
Nuclear Magnetic Resonance NMR is probably the most useful and powerful technique for identifying and characterizing organic compounds. Felix Bloch and Edward Mills Purcell were awarded the 1952 Nobel
More informationNuclear Shielding and 1. H Chemical Shifts. 1 H NMR Spectroscopy Nuclear Magnetic Resonance
NMR Spectroscopy Nuclear Magnetic Resonance Nuclear Shielding and hemical Shifts What do we mean by "shielding?" What do we mean by "chemical shift?" The electrons surrounding a nucleus affect the effective
More informationTrans Fats. What is a trans fat? Trans fatty acids, or trans fats as they are known, are certain
Trans Fats What is a trans fat? Trans fatty acids, or trans fats as they are known, are certain fats found in such foodstuffs as vegetable shortenings, margarines, crackers, candies baked goods and many
More informationAS COMPETITION PAPER 2008
AS COMPETITION PAPER 28 Name School Town & County Total Mark/5 Time Allowed: One hour Attempt as many questions as you can. Write your answers on this question paper. Marks allocated for each question
More informationRotational-Echo, Double-Resonance NMR
73 Rotational-Echo, Double-Resonance NMR Terry Gullion Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA Introduction Rotational-echo, double-resonance REDOR NMR is a high-resolution,
More informationCHAPTER 4: Enzyme Structure ENZYMES
CHAPTER 4: ENZYMES Enzymes are biological catalysts. There are about 40,000 different enzymes in human cells, each controlling a different chemical reaction. They increase the rate of reactions by a factor
More informationMolecular Models Experiment #1
Molecular Models Experiment #1 Objective: To become familiar with the 3-dimensional structure of organic molecules, especially the tetrahedral structure of alkyl carbon atoms and the planar structure of
More informationBaohui Li, Lu Xu, Qiang Wu, Tiehong Chen, Pingchuan Sun,*, Qinghua Jin, Datong Ding, Xiaoliang Wang, Gi Xue,*, and An-Chang Shi,
5776 Macromolecules 2007, 40, 5776-5786 Various Types of Hydrogen Bonds, Their Temperature Dependence and Water-Polymer Interaction in Hydrated Poly(Acrylic Acid) as Revealed by 1 H Solid-State NMR Spectroscopy
More informationNuclear Magnetic Resonance (NMR) Spectroscopy cont... Recommended Reading:
Applied Spectroscopy Nuclear Magnetic Resonance (NMR) Spectroscopy cont... Recommended Reading: Banwell and McCash Chapter 7 Skoog, Holler Nieman Chapter 19 Atkins, Chapter 18 Relaxation processes We need
More informationThe Role of Electric Polarization in Nonlinear optics
The Role of Electric Polarization in Nonlinear optics Sumith Doluweera Department of Physics University of Cincinnati Cincinnati, Ohio 45221 Abstract Nonlinear optics became a very active field of research
More informationLongitudinal Relaxation Time (T 1 ) Measurement for 1 H on VnmrJ2.2D (use on Ra, Mut, and Isis)
Longitudinal Relaxation Time (T 1 ) Measurement for 1 H on VnmrJ2.2D (use on Ra, Mut, and Isis) Knowledge of the T 1 's of a molecule is important in the setup of many 1D and 2D experiments, in which the
More information1 Introduction to NMR Spectroscopy
Introduction to NMR Spectroscopy Tremendous progress has been made in NMR spectroscopy with the introduction of multidimensional NMR spectroscopy and pulse Fourier transform NMR spectroscopy. For a deeper
More informationElectron Paramagnetic (Spin) Resonance
Electron Paramagnetic (Spin) Resonance References: Jardetzky & Jardetzky, Meth. Biochem. Anal. 9, 235. Wertz & Bolton, Electron Spin Resonance Poole, Electron Spin Resonance... Abragam & Bleaney, EPR of
More informationChapter 2 NMR in Inhomogeneous Fields
Chapter 2 NMR in Inhomogeneous Fields Federico Casanova and Juan Perlo 2.1 Introduction Besides the redesigning of the hardware to excite and detect NMR signals from sample volumes external to the sensor,
More informationSPINS: A Laboratory Information Management System for Archiving. Intermediate and Final Results from NMR Protein Structure. Determinations.
Supplementary Material for: SPINS: A Laboratory Information Management System for Archiving Intermediate and Final Results from NMR Protein Structure Determinations. Michael Baran a, Hunter N. B. Moseley
More informationSingle-scan longitudinal relaxation measurements in high-resolution NMR spectroscopy
Journal of Magnetic Resonance 164 (2003) 321 328 www.elsevier.com/locate/jmr Single-scan longitudinal relaxation measurements in high-resolution NMR spectroscopy Nikolaus M. Loening, a, * Michael J. Thrippleton,
More informationThe Four Questions to Ask While Interpreting Spectra. 1. How many different environments are there?
1 H NMR Spectroscopy (#1c) The technique of 1 H NMR spectroscopy is central to organic chemistry and other fields involving analysis of organic chemicals, such as forensics and environmental science. It
More informationNMR Spectroscopy. Applications. Drug design MRI. Food quality. Structural biology. Metabonomics
Applications Drug design MRI Food qualit Metabonomics Structural biolog Basic Principles N.M.R. = Nuclear Magnetic Resonance Spectroscopic technique, thus relies on the interaction between material and
More informationChapter 2 Polar Covalent Bonds: Acids and Bases
John E. McMurry www.cengage.com/chemistry/mcmurry Chapter 2 Polar Covalent Bonds: Acids and Bases Modified by Dr. Daniela R. Radu Why This Chapter? Description of basic ways chemists account for chemical
More information