Category Archives: Simulations

EasySpin Academy (online), Oct 13-15, 2020

Dear EPR community,

We are excited to announce EasySpin Academy 2020, fully online this time. It is a workshop for EasySpin, a MATLAB-based software toolbox for simulating and fitting Electron Paramagnetic Resonance (EPR) spectra – see http://easyspin.org.

The workshop runs from Tuesday October Oct 13 to Thursday Oct 15. Sessions will be held from 7:30am–11:45am PT (10:30am–2:45pm ET, 16:30-20:45 CET) every day.

Each half day has a series of units, and each unit will start with an introduction to a specific topic and will then be followed by hands-on examples. At the end of every day there will be an online Happy Hour.

Instructors include Stefan Stoll (creator of EasySpin), Stephan Pribitzer (active developer), and others.

The workshop is open to everyone. Some experience with EPR spectroscopy is required, but no prior experience with either MATLAB or EasySpin are expected. We will be able to accommodate both beginners and users with EasySpin experience. The workshop starts with the basics of simulating and fitting EPR spectra, and then progressed to more advanced topics such as pulse shaping.

This workshop is a unique opportunity to learn directly from the core developers of EasySpin, to interact with other EPR researchers, to discuss your EPR simulation projects and needs with EasySpin developers, and to provide feedback about desired features for future releases of EasySpin.

For the workshop, you will require a computer with MATLAB and Zoom pre-installed. If you do not have access to a licensed copy of MATLAB, you can download a 30-day trial from http://mathworks.com. Zoom is free to use and can be downloaded from https://zoom.us.

The workshop is free of charge.

To register, please visit http://easyspin.org/academy. After registration, you will receive an email with details about the schedule. The registration deadline is October 1st.

We intend to accommodate everyone that signs up; however, we reserve ourselves the right to cap the number of participants if necessary.

If you have any questions, feel free to contact us at academy@easyspin.org.

Best regards

The EasySpin Academy team

EasySpin Academy, Aug 26-28 2019, Seattle

Dear EPR community,

We are excited to announce EasySpin Academy 2019, a 2.5-day workshop for EasySpin, a MATLAB-based software toolbox for simulating and fitting Electron Paramagnetic Resonance (EPR) spectra – see http://easyspin.org.

The workshop will be held at the University of Washington in Seattle. It starts on Monday Aug 26 at 6 pm and ends on Wednesday Aug 28 in the evening. Instructors include Stefan Stoll (creator of EasySpin), Stephan Pribitzer (active developer), and others.

The workshop is open to everyone. Some experience with EPR spectroscopy is required, but no prior experience with either MATLAB or EasySpin are expected. We will be able to accommodate both beginners and users with EasySpin experience.

This workshop is a unique opportunity to learn directly from the core developers of EasySpin, to interact with other EPR researchers, to discuss your EPR simulation projects and needs with EasySpin developers, and to provide feedback about desired features for future releases of EasySpin.

For the workshop, bring your own laptop with MATLAB pre-installed. If you do not have access to a licensed copy of MATLAB, you can download a 30-day trial from http://mathworks.com.

The registration fee is $295 and covers three nights in on-campus double-occupancy dorm rooms (Monday, Tuesday, Wednesday) and all meals during the workshop.

To register, please visit http://easyspin.org/academy. After registration, you will received an email with details about the payment. The registration deadline is July 25.

There are only a limited number of slots available, and they will be allocated on a first-come, first-served basis.

Best regards

Stefan Stoll

De novo prediction of cross-effect efficiency for magic angle spinning dynamic nuclear polarization #DNPNMR

Mentink-Vigier, Frédéric, Anne-Laure Barra, Johan van Tol, Sabine Hediger, Daniel Lee, and Gaël De Paëpe. “De Novo Prediction of Cross-Effect Efficiency for Magic Angle Spinning Dynamic Nuclear Polarization.” Physical Chemistry Chemical Physics 21, no. 4 (2019): 2166–76.

https://doi.org/10.1039/C8CP06819D.

Magic angle spinning dynamic nuclear polarization (MAS-DNP) has become a key approach to boost the intrinsic low sensitivity of NMR in solids. This method relies on the use of both stable radicals as polarizing agents (PAs) and suitable high frequency microwave irradiation to hyperpolarize nuclei of interest. Relating PA chemical structure to DNP efficiency has been, and is still, a long-standing problem. The complexity of the polarization transfer mechanism has so far limited the impact of analytical derivation. However, recent numerical approaches have profoundly improved the basic understanding of the phenomenon and have now evolved to a point where they can be used to help design new PAs. In this work, the potential of advanced MAS-DNP simulations combined with DFT calculations and high-field EPR to qualitatively and quantitatively predict hyperpolarization efficiency of particular PAs is analyzed. This approach is demonstrated on AMUPol and TEKPol, two widely-used bis-nitroxide PAs. The results notably highlight how the PA structure and EPR characteristics affect the detailed shape of the DNP field profile. We also show that refined simulations of this profile using the orientation dependency of the electron spin–lattice relaxation times can be used to estimate the microwave B1 field experienced by the sample. Finally, we show how modelling the nuclear spin–lattice relaxation times of close and bulk nuclei while accounting for PA concentration allows for a prediction of DNP enhancement factors and hyperpolarization build-up times.

Large-scale ab initio simulations of MAS DNP enhancements using a Monte Carlo optimization strategy #DNPNMR

Perras, Frédéric A., and Marek Pruski. “Large-Scale Ab Initio Simulations of MAS DNP Enhancements Using a Monte Carlo Optimization Strategy.” The Journal of Chemical Physics 149, no. 15 (October 21, 2018): 154202.

https://doi.org/10.1063/1.5042651

Magic-angle-spinning (MAS) dynamic nuclear polarization (DNP) has recently emerged as a powerful technology enabling otherwise unrealistic solid-state NMR experiments. The simulation of DNP processes which might, for example, aid in refining the experimental conditions or the design of better performing polarizing agents, is, however, plagued with significant challenges, often limiting the system size to only 3 spins. Here, we present the first approach to fully ab initio large-scale simulations of MAS DNP enhancements. The Landau-Zener equation is used to treat all interactions concerning electron spins, and the low-order correlations in the Liouville space method is used to accurately treat the spin diffusion, as well as its MAS speed dependence. As the propagator cannot be stored, a Monte Carlo optimization method is used to determine the steady-state enhancement factors. This new software is employed to investigate the MAS speed dependence of the enhancement factors in large spin systems where spin diffusion is of importance, as well as to investigate the impacts of solvent and polarizing agent deuteration on the performance of MAS DNP.

Conformation of Bis-nitroxide Polarizing Agents by Multi- frequency EPR Spectroscopy #DNPNMR

To optimize the DNP process it is crucial to understand the EPR properties of the polarizing agents. This article demonstrates the need of multi-frequency, high-field EPR spectroscopy to gain a deep understanding of all EPR parameters and how they influence the DNP process.

Soetbeer, Janne, Peter Gast, Joseph J Walish, Yanchuan Zhao, Christy George, Chen Yang, Timothy M Swager, Robert G Griffin, and Guinevere Mathies. “Conformation of Bis-Nitroxide Polarizing Agents by Multi- Frequency EPR Spectroscopy,”

http://dx.doi.org/10.1039/C8CP05236K

The chemical structure of polarizing agents critically determines the efficiency of dynamic nuclear polarization (DNP). For cross-effect DNP, biradicals are the polarizing agents of choice and the interaction and relative orientation of the two unpaired electrons should be optimal. Both parameters are affected by the molecular structure of the biradical in the frozen glassy matrix that is typically used for DNP/MAS NMR and likely differs from the structure observed with X-ray crystallography. We have determined the conformations of six bis-nitroxide polarizing agents, including the highly efficient AMUPol, in their DNP matrix with EPR spectroscopy at 9.7 GHz, 140 GHz, and 275 GHz. The multi-frequency approach in combination with an advanced fitting routine allows us to reliably extract the interaction and relative orientation of the nitroxide moieties. We compare the structures of six bis-nitroxides to their DNP performance at 500 MHz/330 GHz.

Many-body kinetics of dynamic nuclear polarization by the cross effect #DNPNMR

Karabanov, A., D. Wiśniewski, F. Raimondi, I. Lesanovsky, and W. Köckenberger. “Many-Body Kinetics of Dynamic Nuclear Polarization by the Cross Effect.” Physical Review A 97 (26 2018): 031404.

https://doi.org/10.1103/PhysRevA.97.031404.

Dynamic nuclear polarization (DNP) is an out-of-equilibrium method for generating nonthermal spin polarization which provides large signal enhancements in modern diagnostic methods based on nuclear magnetic resonance. A particular instance is cross-effect DNP, which involves the interaction of two coupled electrons with the nuclear spin ensemble. Here we develop a theory for this important DNP mechanism and show that the nonequilibrium nuclear polarization buildup is effectively driven by three-body incoherent Markovian dissipative processes involving simultaneous state changes of two electrons and one nucleus.We identify different parameter regimes for effective polarization transfer and discuss under which conditions the polarization dynamics can be simulated by classical kinetic Monte Carlo methods. Our theoretical approach allows simulations of the polarization dynamics on an individual spin level for ensembles consisting of hundreds of nuclear spins. The insight obtained by these simulations can be used to find optimal experimental conditions for cross-effect DNP and to design tailored radical systems that provide optimal DNP efficiency.

[NMR] PhD and Postdoctoral positions available to join the Emsley group at EPFL #DNPNMR

PhD and Postdoctoral positions available to join the Emsley group at EPFL, Lausanne


We are looking for highly motivated candidates to take up PhD and Postdoctoral positions developing new methods in NMR spectroscopy to address challenging problems in chemistry and materials science. In particular we will be working on extending dynamic nuclear polarization enhanced NMR crystallography to complex non-crystalline materials. Examples of our recent work and the application areas that we work on can be found on our website: http://lrm.epfl.ch


We are looking for highly motivated candidates with strong scientific background, independence, and who enjoy teamwork. You should hold a relevant qualification in chemistry, physics or related disciplines. Skills in one of the following fields of expertise are a plus:


• Experimental multi-dimensional nuclear magnetic resonance,
• 
Simulation, Theory, or Modelling of nuclear spin dynamics, NMR properties or chemical structures.
 

Our laboratory at EPFL is part of one the world’s leading chemistry departments, and is located Lausanne on the north shore of Lake Geneva. The laboratory is equipped with unique state of the art NMR spectrometers (including gyrotron DNP accessories at 400 and 900 MHz, a dissolution-DNP machine, and 100 kHz magic angle spinning probes).

 
Motivated candidates should contact Lyndon Emsley by email to lyndon.emsley@epfl.ch


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Magic angle spinning NMR below 6 K with a computational fluid dynamics analysis of fluid flow and temperature gradients

This article is not specifically about DNP spectroscopy. However, magic angle spinning at 6K is definitely of interest to DNP, especially when using low-power, solid-state microwave sources.

Sesti, E.L., et al., Magic angle spinning NMR below 6 K with a computational fluid dynamics analysis of fluid flow and temperature gradients. J. Magn. Reson., 2018. 286(Supplement C): p. 1-9.

http://www.sciencedirect.com/science/article/pii/S1090780717302689

We report magic angle spinning (MAS) up to 8.5 kHz with a sample temperature below 6 K using liquid helium as a variable temperature fluid. Cross polarization 13C NMR spectra exhibit exquisite sensitivity with a single transient. Remarkably, 1H saturation recovery experiments show a 1H T1 of 21 s with MAS below 6 K in the presence of trityl radicals in a glassy matrix. Leveraging the thermal spin polarization available at 4.2 K versus 298 K should result in 71 times higher signal intensity. Taking the 1H longitudinal relaxation into account, signal averaging times are therefore predicted to be expedited by a factor of >500. Computer assisted design (CAD) and finite element analysis were employed in both the design and diagnostic stages of this cryogenic MAS technology development. Computational fluid dynamics (CFD) models describing temperature gradients and fluid flow are presented. The CFD models bearing and drive gas maintained at 100 K, while a colder helium variable temperature fluid stream cools the center of a zirconia rotor. Results from the CFD were used to optimize the helium exhaust path and determine the sample temperature. This novel cryogenic experimental platform will be integrated with pulsed dynamic nuclear polarization and electron decoupling to interrogate biomolecular structure within intact human cells.

Fast and accurate MAS-DNP simulations of large spin ensembles #DNPNMR

Mentink-Vigier, F., S. Vega, and G. De Paepe, Fast and accurate MAS-DNP simulations of large spin ensembles. Phys. Chem. Chem. Phys., 2017. 19(5): p. 3506-3522.

https://www.ncbi.nlm.nih.gov/pubmed/28093594

A deeper understanding of parameters affecting Magic Angle Spinning Dynamic Nuclear Polarization (MAS-DNP), an emerging nuclear magnetic resonance hyperpolarization method, is crucial for the development of new polarizing agents and the successful implementation of the technique at higher magnetic fields (>10 T). Such progress is currently impeded by computational limitation which prevents the simulation of large spin ensembles (electron as well as nuclear spins) and to accurately describe the interplay between all the multiple key parameters at play. In this work, we present an alternative approach to existing cross-effect and solid-effect MAS-DNP codes that yields fast and accurate simulations. More specifically we describe the model, the associated Liouville-based formalism (Bloch-type derivation and/or Landau-Zener approximations) and the linear time algorithm that allows computing MAS-DNP mechanisms with unprecedented time savings. As a result, one can easily scan through multiple parameters and disentangle their mutual influences. In addition, the simulation code is able to handle multiple electrons and protons, which allows probing the effect of (hyper)polarizing agents concentration, as well as fully revealing the interplay between the polarizing agent structure and the hyperfine couplings, nuclear dipolar couplings, nuclear relaxation times, both in terms of depolarization effect, but also of polarization gain and buildup times.

Multiscale computational modeling of (13)C DNP in liquids #DNPNMR

Kucuk, S.E. and D. Sezer, Multiscale computational modeling of (13)C DNP in liquids. Phys Chem Chem Phys, 2016. 18(14): p. 9353-7.

http://www.ncbi.nlm.nih.gov/pubmed/27001446

Dynamic nuclear polarization (DNP) enables the substantial enhancement of the NMR signal intensity in liquids. While proton DNP is dominated by the dipolar interaction between the electron and nuclear spins, the Fermi contact (scalar) interaction is equally important for heavier nuclei. The impossibility to predict the magnitude and field dependence of the scalar contribution hampers the application of high-field DNP to nuclei other than (1)H. We demonstrate that molecular dynamics (MD) simulations followed by density functional calculations of the Fermi contacts along the MD trajectory lead to quantitative agreement with the DNP coupling factors of the methyl and carbonyl carbons of acetone in water at 0.35 T. Thus, the accurate calculation of scalar-dominated DNP enhancement at a desired magnetic field is demonstrated for the first time. For liquid chloroform at fields above 9 T, our methodology predicts direct (13)C DNP enhancements that are two orders of magnitude larger than those of (1)H.

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