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Virtual NMR Spectrometer a software package for accurate and efficient calculation of the outcome of NMR experiments and a computer tool for learning NMR . David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park. 90 o. 90 o. t1. d1.

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David fushman department of chemistry biochemistry university of maryland college park l.jpg

Virtual NMR Spectrometera software package for accurate andefficient calculation of the outcome of NMR experiments and a computer tool for learning NMR

David Fushman

Department of Chemistry & Biochemistry

University of Maryland, College Park


Why do we need computer simulations in nmr l.jpg

90o

90o

t1

d1

Why do we need computer simulations in NMR?

3D CT-HN(CA)CB, Shan et al., 1996, JACS 118, 6570


Why do we need computer simulations in nmr3 l.jpg

Why do we need computer simulations in NMR?

 Modern multidimensional NMR experiments involve pulse-field gradients, shaped RF pulses, off-resonance effects, complex decoupling schemes, and much more

it has become practically impossible to accurately predict the outcome

of these complicated pulse sequences under real conditions

 We need to be able to optimize experimental conditions with minimal cost of NMR time (especially for 3D, 4D expts)

 We need efficient tools for designing new pulse sequences (especially for multidimensional expts)

 Learning NMR -- Difficulties in understanding theoretical aspects of NMR

– Practical aspects: insufficient access to NMR instruments


Real experimental conditions can be far from ideal conditions l.jpg

We have theoretical approaches that allow us to

accurately predict the outcome of many NMR

experiments under ideal conditions, but…

Real experimental conditions can be far from ideal conditions

Pulse imperfectionsOff-resonance effectsSpin relaxationExchange phenomena Water suppression etc


Vnmr the virtual nmr spectrometer l.jpg

Introducing

VNMR – The Virtual NMR Spectrometer

A NMR spectrometer that you can carry in your bag


Vnmr the virtual nmr spectrometer flowchart of the virtual spectrometer l.jpg

VNMR – The Virtual NMR SpectrometerFlowchart of the Virtual Spectrometer

Experimental or user-designed pulse sequence

TRANSLATOR

SIMULATOR

NMR ‘Experiment’:

Preparation

Evolution

Data Acquisition

DATA PROCESSING

1D or nD Spectra

Experimental Conditions

Spin System Setup

Input

Output

Calculation


Vnmr treatment of spin evolution l.jpg

VNMR: Treatment of spin evolution

Spin Density Evolution:

Spin Hamiltonian in the rotating frame:

Spin Relaxation, Cross-relaxation, Chem.Exchange etc:


Vnmr basic goals l.jpg

VNMR – Basic Goals

Accuracy and efficiency in simulation of various pulse sequences, including PFG and shaped RF pulses

The ability to execute the actual pulse sequences from the spectrometer

Ease of use (intuitive GUI, no programming skills, OS/platform independence)

Flexibility in selecting various spin systems and experimental conditions

Tools for data processing, analysis, and visualization


Vnmr 3 1 pre beta highlight of basic features l.jpg

VNMR 3.1 (pre-beta) – Highlight of Basic Features

1D, 2D, almost finished 3D

Translator (Bruker  VNMR) allows “running” actual pulse sequences

Simulation of various pulse sequences, including PFG and shaped RF pulses

Data processing, analysis, and visualization of the results

Shaped pulse generator

Tracing/visualization of spin-density components

Relaxation calculator

Save/load capabilities

Converters to basic NMR processing packages: XWINNMR, (nmrPIPE)

Experimental noise


Virtual nmr spectrometer a tool for in silico nmr l.jpg

Virtual NMR Spectrometera tool for in silico NMR


A simple example cosy l.jpg

90o

90o

acq

t1

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30

b

b’

20

12

a

A simple example – COSY

3-spin system:

Jab = 20 Hz

Jab’ = 12 Hz

Jb’b = 30 Hz

Ha = 4.2 ppm

Hb = 2.8 ppm

Hb’ = 3.3 ppm


A simple example homonuclear cosy l.jpg

90o

90o

acq

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A simple example: Homonuclear COSY

ns = 1

ns = 8

Suppression of the axial noise


Another example dqf cosy l.jpg

90o

90o

90o

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t1

Another example – DQF COSY

3-spin DQF COSY



Nmr experiments involving pulsed field gradients l.jpg

90o

90o

acq

d1

t1

1H

G

NMR Experiments Involving Pulsed Field Gradients

Next example: Gradient-selective COSY (cosygs)

How to treat gradients accurately?


Gradient treatment salami model l.jpg

z

3

L

2

Lmin

Bo’= Bo+G.z

1

Z

Magnetic field gradient along the z-axis

Orientation of magnetization vectors

Representation of NMR sample as a set of layers

nz=0

Lmin/2

-1

-2

-3

0

-Lmin/2

NMR Experiments Involving Pulsed Field Gradients

Gradient treatment – ‘Salami’ model


Gradient treatment flowchart l.jpg

First PFG

Initialization:

Calculate Ba, Hevol, R

Initialize spin density: s1= seq

Set i = 1; GRAD=off

Gradient treatment flowchart

Calculate Hi, si+1

Increment i

N

GRAD=on ?

Y

CTP

Salami

Split si into NL layers

For each layer nz

Calculate Hi(nz), si+1(nz)

Store si+1(nz)

Increment i

Calculate Hi ,si+1

Calculate T, then wi, ki

Increment i

End of pulse sequence?

End of pulse sequence?

N

N

Y

Y

Integrate s

Average s

Acquisition

Increment ns and phases

N

ns > NS ?

Y

Stop


Gradient selection of p or n type coherences or both l.jpg

90o

90o

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1H

G

Gradient selection of P- or N- type coherences or both


Another example decoupled 1 h 15 n hsqc l.jpg

90o

180o

acq

d1

1H

t1/2

t1/2

15N

dec

Another example -- decoupled 1H-15N HSQC


Closer to reality differential line broadening l.jpg

 

DD +CSA





DD - CSA



Closer to reality – differential line broadening


Relaxation calculator l.jpg

Relaxation calculator

In order to reconstruct the actual experimental conditions, we need to be able to use spin-relaxation parameters as close as possible to the reality


Coupled 1 h 15 n hsqc l.jpg

90o

180o

acq

d1

1H

t1/2

t1/2

15N

dec

Coupled 1H-15N HSQC


1 h 15 n hsqc coupled decoupled l.jpg

90o

90o

180o

180o

acq

acq

d1

d1

1H

1H

t1/2

t1/2

t1/2

t1/2

15N

15N

dec

dec

1H-15N HSQC coupled/decoupled

Now with differential line widths


Hsqc example l.jpg

Projections displayallows tracking of user-selected components of the spin density in the course of NMR experiment, for testing and educational purposes

HSQC example


Trosy simulation l.jpg

TROSYsimulation


Transverse relaxation optimized spectroscopy trosy l.jpg

 

DD +CSA





DD - CSA



Transverse-Relaxation Optimized SpectroscopY (TROSY)

Using the interference between Dipolar interaction and CSA


Virtual spectrometer web site www vsnmr org l.jpg

Virtual Spectrometer Web Site:www.vsnmr.org

Coming soon:

Beta-testing version

Demo versions for students


Vnmr as nmr learning tool l.jpg

VNMR as NMR learning tool

Easiness of use and broad accessibility:

It does not require programming skills

Even more so -- you don’t need a spectrometer!!!

Intuitive User Interface

Compatibility with Bruker programming language

Future plans: Web access

Demo versions

Set of basic NMR experiments


Acknowledgements l.jpg

Acknowledgements

David Cowburn (Rockefeller U.)

Vlad Ruchinsky (Yale U.)

Peter Nicholas (UNC Medical School)

Konstantin Berlin (U.Maryland)

Grant Support:

Camille & Henry Dreyfus Foundation

National Science Foundation


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