EPR Spectroscopy in Chemistry and Biology

A special issue of Magnetochemistry (ISSN 2312-7481). This special issue belongs to the section "Magnetic Resonances".

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 21409

Special Issue Editors


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Guest Editor
Weizmann Institute of Science, Rehovot, Israel
Interests: electron paramagnetic resonance (EPR); double electron-electron resonance (DEER); hyperfine spectroscopy; metal ions; bioinorganic chemistry
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Guest Editor
Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
Interests: electromagnetism; spin physics; EPR spectroscopy; structural biology; spin labels

Special Issue Information

Dear Colleagues,

Electron paramagnetic resonance (EPR or synonymously ESR) has proven to be a spectroscopic technique of great significance in understanding structural elements in chemical and biological organizations. Particularly, EPR-based distance measurements and hyperfine spectroscopic techniques together with traditional continuous-wave EPR (cw-EPR) can offer, respectively, a plethora of long (2–8 nm) and short (<1 nm) range structural information which is challenging to obtain with other techniques.

This Special Issue is devoted to EPR applications in Chemistry and Biology, as well as to relevant methodological developments, facilitated by improved hardware, new pulse sequences, and new EPR spin labels.

Dr. Angeliki Giannoulis
Dr. Dinar Abdullin
Guest Editors

Manuscript Submission Information

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Keywords

  • electron paramagnetic resonance (EPR/ESR)
  • chemical model systems
  • structural biology
  • proteins
  • distance measurements
  • double electron–electron resonance (DEER/PELDOR)
  • continuous-wave EPR (cw-EPR)
  • hyperfine spectroscopy
  • paramagnetic metal ions
  • spin labels
  • pulse sequences
  • arbitrary waveform generators (AWG) units

Published Papers (6 papers)

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Research

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14 pages, 1376 KiB  
Article
A Low-Spin CoII/Nitroxide Complex for Distance Measurements at Q-Band Frequencies
by Angeliki Giannoulis, David B. Cordes, Alexandra M. Z. Slawin and Bela E. Bode
Magnetochemistry 2022, 8(4), 43; https://doi.org/10.3390/magnetochemistry8040043 - 11 Apr 2022
Cited by 1 | Viewed by 2611
Abstract
Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is continuously furthering the understanding of chemical and biological assemblies through distance measurements in the nanometer range. New paramagnets and pulse sequences can provide structural insights not accessible through other techniques. In the pursuit of alternative [...] Read more.
Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is continuously furthering the understanding of chemical and biological assemblies through distance measurements in the nanometer range. New paramagnets and pulse sequences can provide structural insights not accessible through other techniques. In the pursuit of alternative spin centers for PDS, we synthesized a low-spin CoII complex bearing a nitroxide (NO) moiety, where both the CoII and NO have an electron spin S of 1/2. We measured CoII-NO distances with the well-established double electron–electron resonance (DEER aka PELDOR) experiment, as well as with the five- and six-pulse relaxation-induced dipolar modulation enhancement (RIDME) spectroscopies at Q-band frequencies (34 GHz). We first identified challenges related to the stability of the complex in solution via DEER and X-ray crystallography and showed that even in cases where complex disproportionation is unavoidable, CoII-NO PDS measurements are feasible and give good signal-to-noise (SNR) ratios. Specifically, DEER and five-pulse RIDME exhibited an SNR of ~100, and while the six-pulse RIDME exhibited compromised SNR, it helped us minimize unwanted signals from the RIDME traces. Last, we demonstrated RIDME at a 10 μM sample concentration. Our results demonstrate paramagnetic CoII to be a feasible spin center in medium magnetic fields with opportunities for PDS studies involving CoII ions. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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15 pages, 4200 KiB  
Article
EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory
by Maria Drosou, Christiana A. Mitsopoulou, Maylis Orio and Dimitrios A. Pantazis
Magnetochemistry 2022, 8(4), 36; https://doi.org/10.3390/magnetochemistry8040036 - 23 Mar 2022
Cited by 7 | Viewed by 5660
Abstract
Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for [...] Read more.
Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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13 pages, 2046 KiB  
Article
Hyperfine Decoupling of ESR Spectra Using Wavelet Transform
by Aritro Sinha Roy and Madhur Srivastava
Magnetochemistry 2022, 8(3), 32; https://doi.org/10.3390/magnetochemistry8030032 - 08 Mar 2022
Cited by 9 | Viewed by 3017
Abstract
The objective of spectral analysis is to resolve and extract relevant features from experimental data in an optimal fashion. In continuous-wave (cw) electron spin resonance (ESR) spectroscopy, both g values of a paramagnetic center and hyperfine splitting (A) caused by its [...] Read more.
The objective of spectral analysis is to resolve and extract relevant features from experimental data in an optimal fashion. In continuous-wave (cw) electron spin resonance (ESR) spectroscopy, both g values of a paramagnetic center and hyperfine splitting (A) caused by its interaction with neighboring magnetic nuclei in a molecule provide important structural and electronic information. However, in the presence of g- and/or A-anisotropy and/or large number of resonance lines, spectral analysis becomes highly challenging. Either high-resolution experimental techniques are employed to resolve the spectra in those cases or a range of suitable ESR frequencies are used in combination with simulations to identify the corresponding g and A values. In this work, we present a wavelet transform technique in resolving both simulated and experimental cw-ESR spectra by separating the hyperfine and super-hyperfine components. We exploit the multiresolution property of wavelet transforms that allow the separation of distinct features of a spectrum based on simultaneous analysis of spectrum and its varying frequency. We retain the wavelet components that stored the hyperfine and/or super-hyperfine features, while eliminating the wavelet components representing the remaining spectrum. We tested the method on simulated cases of metal–ligand adducts at L-, S-, and X-band frequencies, and showed that extracted g values, hyperfine and super-hyperfine coupling constants from simulated spectra, were in excellent agreement with the values of those parameters used in the simulations. For the experimental case of a copper(II) complex with distorted octahedral geometry, the method was able to extract g and hyperfine coupling constant values, and revealed features that were buried in the overlapped spectra. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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13 pages, 1088 KiB  
Article
Electronic Structure of Tyrosyl D Radical of Photosystem II, as Revealed by 2D-Hyperfine Sublevel Correlation Spectroscopy
by Maria Chrysina, Georgia Zahariou, Nikolaos Ioannidis, Yiannis Sanakis and George Mitrikas
Magnetochemistry 2021, 7(9), 131; https://doi.org/10.3390/magnetochemistry7090131 - 21 Sep 2021
Cited by 1 | Viewed by 1827
Abstract
The biological water oxidation takes place in Photosystem II (PSII), a multi-subunit protein located in thylakoid membranes of higher plant chloroplasts and cyanobacteria. The catalytic site of PSII is a Mn4Ca cluster and is known as the oxygen evolving complex (OEC) [...] Read more.
The biological water oxidation takes place in Photosystem II (PSII), a multi-subunit protein located in thylakoid membranes of higher plant chloroplasts and cyanobacteria. The catalytic site of PSII is a Mn4Ca cluster and is known as the oxygen evolving complex (OEC) of PSII. Two tyrosine residues D1-Tyr161 (YZ) and D2-Tyr160 (YD) are symmetrically placed in the two core subunits D1 and D2 and participate in proton coupled electron transfer reactions. YZ of PSII is near the OEC and mediates electron coupled proton transfer from Mn4Ca to the photooxidizable chlorophyll species P680+. YD does not directly interact with OEC, but is crucial for modulating the various S oxidation states of the OEC. In PSII from higher plants the environment of YD radical has been extensively characterized only in spinach (Spinacia oleracea) Mn-depleted non functional PSII membranes. Here, we present a 2D-HYSCORE investigation in functional PSII of spinach to determine the electronic structure of YD radical. The hyperfine couplings of the protons that interact with the YD radical are determined and the relevant assignment is provided. A discussion on the similarities and differences between the present results and the results from studies performed in non functional PSII membranes from higher plants and PSII preparations from other organisms is given. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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Review

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38 pages, 4819 KiB  
Review
Probing Small-Angle Molecular Motions with EPR Spectroscopy: Dynamical Transition and Molecular Packing in Disordered Solids
by Sergei A. Dzuba
Magnetochemistry 2022, 8(2), 19; https://doi.org/10.3390/magnetochemistry8020019 - 27 Jan 2022
Cited by 3 | Viewed by 2461
Abstract
Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of [...] Read more.
Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of dynamics and structure of disordered solids still does not exist, and only some phenomenological models can be developed to explain results of particular experiments. Among different experimental approaches, electron paramagnetic resonance (EPR) applied to spin probes and labels also can deliver useful information. EPR allows probing small-angle orientational molecular motions (molecular librations), which intrinsically are inherent to all molecular solids. EPR is employed in its conventional continuous wave (CW) and pulsed—electron spin echo (ESE)—versions. CW EPR spectra are sensitive to dynamical librations of molecules while ESE probes stochastic molecular librations. In this review, different manifestations of small-angle motions in EPR of spin probes and labels are discussed. It is shown that CW-EPR-detected dynamical librations provide information on dynamical transition in these media, similar to that explored with neutron scattering, and ESE-detected stochastic librations allow elucidating some features of nanoscale molecular packing. The possible EPR applications are analyzed for gel-phase lipid bilayers, for biological membranes interacting with proteins, peptides and cryoprotectants, for supercooled ionic liquids (ILs) and supercooled deep eutectic solvents (DESs), for globular proteins and intrinsically disordered proteins (IDPs), and for some other molecular solids. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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18 pages, 4451 KiB  
Review
The Advantages of EPR Spectroscopy in Exploring Diamagnetic Metal Ion Binding and Transfer Mechanisms in Biological Systems
by Shelly Meron, Yulia Shenberger and Sharon Ruthstein
Magnetochemistry 2022, 8(1), 3; https://doi.org/10.3390/magnetochemistry8010003 - 26 Dec 2021
Cited by 5 | Viewed by 3749
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving [...] Read more.
Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving cellular mechanisms, involving small ligand binding or metal ion transfer, is not trivial and cannot be studied using conventional biophysical tools. In recent years, our group has been using EPR spectroscopy to study the mechanism underlying copper ion transfer in eukaryotic and prokaryotic systems. This mini-review focuses on our achievements following copper metal coordination in the diamagnetic oxidation state, Cu(I), between biomolecules. We discuss the conformational changes induced in proteins upon Cu(I) binding, as well as the conformational changes induced in two proteins involved in Cu(I) transfer. We also consider how EPR spectroscopy, together with other biophysical and computational tools, can identify the Cu(I)-binding sites. This work describes the advantages of EPR spectroscopy for studying biological processes that involve small ligand binding and transfer between intracellular proteins. Full article
(This article belongs to the Special Issue EPR Spectroscopy in Chemistry and Biology)
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