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Advances in Photosynthesis and Respiration
Biophysical Techniques in Photosynthesis Volume II Advances in Photosynthesis and Respiration VOLUME 26 Series Editor: GOVINDJEE University of Illinois, Urbana, Illinois, U.S.A. Consulting Editors: Julian EATON-RYE, Dunedin, New Zealand Christine H. FOYER, Newcastle upon Tyne, U.K. David B. KNAFF, Lubbock, Texas, U.S.A. Anthony L. MOORE, Brighton, U.K. Sabeeha MERCHANT, Los Angeles, California, U.S.A. Krishna NIYOGI, Berkeley, California, U.S.A. William PARSON, Seatle, Washington, U.S.A. Agepati RAGHAVENDRA, Hyderabad, India Gernot RENGER, Berlin, Germany The scope of our series, beginning with volume 11, reflects the concept that photosynthesis and respiration are intertwined with respect to both the protein complexes involved and to the entire bioenergetic machinery of all life. Advances in Photosynthesis and Respiration is a book series that provides a comprehensive and state-of-the-art account of research in photo- synthesis and respiration. Photosynthesis is the process by which higher plants, algae, and certain species of bacteria transform and store solar energy in the form of energy-rich organic molecules. These compounds are in turn used as the energy source for all growth and reproduction in these and almost all other organisms. As such, virtually all life on the planet ultimately depends on photosynthetic energy conversion. Respiration, which occurs in mitochondrial and bacterial membranes, utilizes energy present in organic molecules to fuel a wide range of metabolic reactions critical for cell growth and development. In addition, many photosynthetic organisms engage in energetically wasteful photorespiration that begins in the chloroplast with an oxygenation reaction catalyzed by the same enzyme responsible for capturing carbon dioxide in photosynthesis. -
Simulation and Theory of Classical Spin Hopping on a Lattice
magnetochemistry Article Simulation and Theory of Classical Spin Hopping on a Lattice Richard Gerst , Rodrigo Becerra Silva and Nicholas J. Harmon * Department of Physics, University of Evansville, Evansville, IN 47722, USA; [email protected] (R.G.); [email protected] (R.B.S.) * Correspondence: [email protected] Abstract: The behavior of spin for incoherently hopping carriers is critical to understand in a variety of systems such as organic semiconductors, amorphous semiconductors, and muon-implanted materials. This work specifically examined the spin relaxation of hopping spin/charge carriers through a cubic lattice in the presence of varying degrees of energy disorder when the carrier spin is treated classically and random spin rotations are suffered during the hopping process (to mimic spin–orbit coupling effects) instead of during the wait time period (which would be more appropriate for hyperfine coupling). The problem was studied under a variety of different assumptions regarding the hopping rates and the random local fields. In some cases, analytic solutions for the spin relaxation rate were obtained. In all the models, we found that exponentially distributed energy disorder led to a drastic reduction in spin polarization losses that fell nonexponentially. Keywords: spintronics; organic semiconductors; hopping transport; spin transport 1. Introduction Citation: Gerst, R.; Becerra Silva, R.; Spin relaxation of carriers has garnered much interest in the past few decades due to Harmon, N.J. Simulation and Theory the prospect of spin electronic or spintronic devices that use spin functionality in addition to of Classical Spin Hopping on a charge functionality. However, most work has been concentrated on band transport [1–5]. -
Photochemically Induced Dynamic Nuclear Polarization of Heteronuclear Singlet Order
Photochemically induced dynamic nuclear polarization of heteronuclear singlet order Kirill F. Sheberstov1,2, Liubov Chuchkova2,3, Yinan Hu1,2, Ivan V. Zhukov4,5, Alexey S. Kiryutin4,5, Artur V. Eshtukov6, Dmitry A. Cheshkov6, Danila A. Barskiy1,2, John W. Blanchard2, Dmitry Budker1,2,7, Konstantin L. Ivanov4,5, Alexandra V. Yurkovskaya4,5 1. Institut für Physik, Johannes Gutenberg Universität-Mainz, 55128 Mainz, Germany 2. Helmholtz-Institut Mainz, GSI Helmholtzzentrum für Schwerionenforschung, 55128 Mainz, Germany 3. Faculté des Sciences Mirande, Université de Bourgogne, Dijon 21078, France 4. International Tomography Center SB RAS, Novosibirsk, 630090, Russia 5. Novosibirsk State University, Novosibirsk, 630090, Russia 6. State Scientific Research Institute of Chemistry and Technology of Organoelement Compounds, 105118, Moscow, Russia 7. University of California at Berkeley, California 94720-7300, USA Abstract Photochemically induced dynamic nuclear polarization (photo-CIDNP) is a method to hyperpolarize nuclear spins using light. In most cases, CIDNP experiments are performed at high magnetic field and the sample is irradiated by light inside a nuclear magnetic resonance (NMR) spectrometer. Here we demonstrate photo-CIDNP hyperpolarization generated in the Earth’s magnetic field and under zero- to ultralow-field (ZULF) conditions. Irradiating a sample for several seconds with inexpensive light-emitting diodes produces a strong hyperpolarization of 1H and 13C nuclear spins enhancing the NMR signals by several hundred times. The hyperpolarized spin states at the Earth’s field and in ZULF are different. In the latter case the state corresponds to singlet order between scalar-coupled 1H-13C nuclear spins. This state has longer lifetime than the state hyperpolarized at Earth’s field. -
Photochemically Induced Dynamic Nuclear Polarization Observed by Solid-State NMR in a Uniformly 13C-Isotope Labeled Photosynthetic Reaction Center
Photochemically induced dynamic nuclear polarization observed by solid-state NMR in a uniformly 13C-isotope labeled photosynthetic reaction center Shubhajit Paul,a Bela E. Bode,b Jörg Matysik,a A. Aliac,d a Universität Leipzig, Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany b EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews, KY16 9ST, Scotland c Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16, D-04107 Leipzig, Germany d Gorlaeus Laboratoria, Leiden Institute of Chemistry, Einsteinweg 55, P.O Box 9502, 2300 RA Leiden, The Netherlands KEYWORDS. Photosynthesis, electron transfer, nuclear polarization, spin diffusion. 1 ABSTRACT. A sample of solubilized and quinone-depleted reaction centers (RC) from the purple bacterium Rhodobacter (R.) sphaeroides wild-type (WT) has been prepared entirely 13C and 15N isotope labelled at all positions of the protein as well as of the cofactors. In this sample, the occurrence of the solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect has been probed by 13C solid-state magic-angle spinning (MAS) NMR under illumination. Under continuous illumination, signal intensities are modified by the three-spin mixing (TSM) mechanism. Time-resolved illumination experiments reveal the occurrence of light-induced nuclear polarization on the time-scale of hundreds of microseconds, initially dominated by the transient polarization of the singlet branch of the radical-pair mechanism (RPM). A first kinetic analysis shows that the lifetime of the polarization from the singlet branch, indicated by the enhanced absorptive intensities of the signals from aliphatic carbons, is significantly extended. -
Dirac Material Graphene
Dirac Material Graphene Elena Sheka Russian Peoples’ Friendship University of Russia Moscow, 117198 Russia [email protected] Abstract. The paper presents author’s view on spin-rooted properties of graphene supported by numerous experimental and calculation evidences. Correlation of odd pz electrons of the honeycomb lattice meets a strict demand “different orbitals for different spins”, which leads to spin polarization of electronic states, on the one hand, and generation of an impressive pool of local spins distributed over the lattice, on the other. These features characterize graphene as a peculiar semimetal with Dirac cone spectrum at particular points of Brillouin zone. However, spin-orbit coupling (SOC), though small but available, supplemented by dynamic SOC caused by electron correlation, transforms graphene-semimetal into graphene-topological insulator (TI). The consequent topological non-triviality and local spins are proposed to discuss such peculiar properties of graphene as high temperature ferromagnetism and outstanding chemical behavior. The connection of these new findings with difficulties met at attempting to convert graphene-TI into semiconductor one is discussed. Key words: graphene, Dirac fermions, quasi-relativistic description, hexagonal honeycomb structure, local spins, open-shell molecules, spin-orbital coupling, quantum spin Hall insulator, high temperature ferromagnetism, chemical activity. 1. Introduction Presented in the current paper concerns three main issues laying the foundation of spin features of graphene: (1) a significant correlation of pz odd electrons, exhibited in terms of spin peculiarities of the unrestricted Hartree-Fock (UHF) solutions, (2) spin-orbital coupling (SOC) and (3) the crucial role of the C=C bond length distribution over the body in exhibiting the spin- based features. -
The Effects of Weak Magnetic Fields on Radical Pairs
Bioelectromagnetics The Effects of Weak Magnetic Fields on Radical Pairs Frank S. Barnes1* and Ben Greenebaum2 1Department of Electricaland Computer Engineering, University of Colorado, Boulder, Colorado 2Department of Physics, University of Wisconsin-Parkside, Kenosha,Wisconsin It is proposed that radical concentrations can be modified by combinations of weak, steady and alternating magnetic fields that modify the population distribution of the nuclear and electronic spin state, the energy levels and the alignment of the magnetic moments of the components of the radical pairs. In low external magnetic fields, the electronic and nuclear angular momentum vectors are coupled by internal forces that outweigh the external fields’ interactions and are characterized in the Hamiltonian by the total quantum number F. Radical pairs form with their unpaired electrons in singlet (S) or triplet (T) states with respect to each other. At frequencies corresponding to the energy separation between the various states in the external magnetic fields, transitions can occur that change the populations of both electron and nuclear states. In addition, the coupling between the nuclei, nuclei and electrons, and Zeeman shifts in the electron and nuclear energy levels can lead to transitions with resonances spanning frequencies from a few Hertz into the megahertz region. For nuclear energy levels with narrow absorption line widths, this can lead to amplitude and frequency windows. Changes in the pair recombination rates can change radical concentrations and modify biological processes. The overall conclusion is that the application of magnetic fields at frequencies ranging from a few Hertz to microwaves at the absorption frequencies observed in electron and nuclear resonance spectroscopy for radicals can lead to changes in free radical concentrations and have the potential to lead to biologically significant changes. -
Exploration of the Close Chemical Space of Tryptophan and Tyrosine
Exploration of the close chemical space of tryptophan and tyrosine reveals importance of hydrophobicity in CW-photo-CIDNP performances Felix Torres1, Alois Renn1, Roland Riek1 5 1Laboratory of Physical Chemistry, ETH Zurich, Zuerich, 8093, Switzerland Correspondence to: Roland Riek ([email protected]) Abstract. Sensitivity being one of the main hurdles of Nuclear Magnetic Resonance (NMR) can be gained by polarization techniques including Chemically Induced Dynamic Nuclear Polarization (CIDNP). Kaptein demonstrated that in CIDNP the polarization arises from the formation and the recombination of a radical pair in a magnetic field. In photo-CIDNP of interest 10 here the radical pair is between a dye and the molecule to be polarized. The polarization obtained is thereby dependent on a complex interplay between the two molecules and their physicochemical properties. Here, we explore continuous wave (CW) photo-CIDNP with a set of ten tryptophan and tyrosine analogues and observe not only signal enhancement of two orders of magnitude for 1H at 600 MHz (corresponding to 10’000 times in measurement time), but also reveal that the hydrophobicity of the molecule appears to be an important factor in the polarisation extent within CW-photo-CIDNP. Furthermore, the small 30 Deleted: d 15 chemical library established indicate the existence of many photo-CIDNP active molecules. Introduction Despite decades of development and impressive technological improvements, sensitivity remains the main hurdle of Nuclear Magnetic Resonance (NMR) spectroscopy and imaging (Ardenkjaer-Larsen et al., 2015). Chemical induced dynamic nuclear polarization (CIDNP) enhances the sensitivity of NMR thanks to out-of-Boltzmann nuclear spin polarization. -
The Scientific Case 67 5
5. The Scientific Case 67 5. Chemistry 5.1 Introduction whereas, including cooperative Panel: magnetic interactions, the U.E. Steiner (Konstanz) In chemistry, the application of modern field of molecular (Chairman) magnetic fields has a long magnetism offers new possibilities R. Bittl (Berlin) tradition and has led to well for structural control by magnetic M. Ernst (Nijmegen) established disciplines and fields. In the following sections O. Kahn (Bordeaux) techniques. Two main purposes in these several areas are discussed using high magnetic fields may be from the point of view of the distinguished; the probing of likely impact of intense magnetic structural and dynamical fields. properties and the controlling of chemical processes and structures. 5.2 Molecular magnetism The ability of a magnetic field to function as a probe is usually based Molecular magnetism is a rather on the exploitation of the field new field of research which has dependence of some property of emerged during the last decade or the chemical substance or system, so. It deals with the physics and including its interaction with chemistry of open-shell radiation; i.e. various kinds of molecules and of molecular spectroscopies, of which NMR is assemblies involving open-shell the most vital and powerful one. units. What characterizes this field Thereby detailed qualitative and of research is its deeply quantitative information can be multidisciplinary character. It gained as to chemical composition brings together organic, inorganic, (chemical analysis) as well as and organometallic synthetic structural and dynamical chemists along with theoreticians, properties. Structural aspects solid state physicists, materials pertain to the characterization of and life scientists. -
Coherent Spin Dynamics of Radical Pairs in Weak Magnetic Fields
Coherent Spin Dynamics of Radical Pairs in Weak Magnetic Fields by Hannah J. Hogben A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Trinity Term 2011 University of Oxford Department of Chemistry Physical and Theoretical Chemistry Laboratory Oriel College Abstract Coherent Spin Dynamics of Radical Pairs in Weak Magnetic Fields Hannah J. Hogben Department of Chemistry Physical and Theoretical Chemistry Laboratory and Oriel College Abstract of a thesis submitted for the degree of Doctor of Philosophy Trinity Term 2011 The outcome of chemical reactions proceeding via radical pair (RP) intermediates can be in- fluenced by the magnitude and direction of applied magnetic fields, even for interaction strengths far smaller than the thermal energy. Sensitivity to Earth-strength magnetic fields has been sug- gested as a biophysical mechanism of animal magnetoreception and this thesis is concerned with simulations of the effects of such weak magnetic fields on RP reaction yields. State-space restriction techniques previously used in the simulation of NMR spectra are here applied to RPs. Methods for improving the efficiency of Liouville-space spin dynamics calculations are presented along with a procedure to form operators directly into a reduced state-space. These are implemented in the spin dynamics software Spinach. Entanglement is shown to be a crucial ingredient for the observation of a low field effect on RP reaction yields in some cases. It is also observed that many chemically plausible initial states possess an inherent directionality which may be a useful source of anisotropy in RP reactions. The nature of the radical species involved in magnetoreception is investigated theoretically. -
Author's Tracked Changes
Exploration of the close chemical space of tryptophan and tyrosine reveals importance of hydrophobicity in CW-photo-CIDNP performances Felix Torres1, Alois Renn1, Roland Riek1 5 1Laboratory of Physical Chemistry, ETH Zurich, Zuerich, 8093, Switzerland Correspondence to: Roland Riek ([email protected]) Abstract. Sensitivity being one of the main hurdles of Nuclear Magnetic Resonance (NMR) can be gained by polarization techniques including Chemically Induced Dynamic Nuclear Polarization (CIDNP). Kaptein demonstrated that the basic mechanism of the CIDNP polarization arises from spin sorting based on coherent electron-electron-nuclear spin dynamics 10 during the formation and the recombination of a radical pair in a magnetic field. In photo-CIDNP of interest here the radical pair is between a dye and the molecule to be polarized. Here, we explore continuous wave (CW) photo-CIDNP with a set of ten tryptophan and tyrosine analogues, many of them newly identified to be photo-CIDNP-active, and observe not only signal enhancement of two orders of magnitude for 1H at 600 MHz (corresponding to 10’000 times in measurement time), but also reveal that polarisation enhancement correlates with the hydrophobicity of the molecules. Furthermore, the small chemical 15 library established indicate the existence of many photo-CIDNP active molecules. Introduction Despite decades of development and impressive technological improvements, sensitivity remains the main hurdle of Nuclear Magnetic Resonance (NMR) spectroscopy and imaging (Ardenkjaer-Larsen et al., 2015). Chemical induced dynamic nuclear polarization (CIDNP) enhances the sensitivity of NMR thanks to out-of-Boltzmann nuclear spin polarization. The first 20 anomalous lines related to CIDNP were serendipitously observed in 1967 independently by Bargon et al. -
Mr-2021-1-Manuscript-Version4.Pdf
Exploration of the close chemical space of tryptophan and tyrosine reveals importance of hydrophobicity in CW-photo-CIDNP performances Felix Torres1, Alois Renn1, Roland Riek1 5 1Laboratory of Physical Chemistry, ETH Zurich, Zuerich, 8093, Switzerland Correspondence to: Roland Riek ([email protected]) Abstract. Sensitivity being one of the main hurdles of Nuclear Magnetic Resonance (NMR) can be gained by polarization techniques including Chemically Induced Dynamic Nuclear Polarization (CIDNP). Kaptein demonstrated that in CIDNP the polarization arises from the formation and the recombination of a radical pair in a magnetic field. In photo-CIDNP of interest 10 here the radical pair is between a dye and the molecule to be polarized. The polarization obtained is thereby dependent on a complex interplay between the two molecules and their physicochemical properties. Here, we explore continuous wave (CW) photo-CIDNP with a set of ten tryptophan and tyrosine analogues and observe not only signal enhancement of two orders of magnitude for 1H at 600 MHz (corresponding to 10’000 times in measurement time), but also reveal that the hydrophobicity of the molecule appears to be an important factor in the polarisation extent within CW-photo-CIDNP. Furthermore, the small 15 chemical library established indicate the existence of many photo-CIDNP active molecules. Introduction Despite decades of development and impressive technological improvements, sensitivity remains the main hurdle of Nuclear Magnetic Resonance (NMR) spectroscopy and imaging (Ardenkjaer-Larsen et al., 2015). Chemical induced dynamic nuclear polarization (CIDNP) enhances the sensitivity of NMR thanks to out-of-Boltzmann nuclear spin polarization. The first 20 anomalous lines related to CIDNP were serendipitously observed in 1967 independently by Ward et al. -
Photochemically Induced Dynamic Nuclear Polarization) Effect Has Been Probed by 13C Solid-State Magic-Angle Spinning (MAS)
CORE Metadata, citation and similar papers at core.ac.uk Provided by St Andrews Research Repository Photochemically induced dynamic nuclear polarization observed by solid-state NMR in a uniformly 13C-isotope labeled photosynthetic reaction center Shubhajit Paul,a Bela E. Bode,b Jörg Matysik,a A. Aliac,d a Universität Leipzig, Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany b EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews, KY16 9ST, Scotland c Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16, D-04107 Leipzig, Germany d Gorlaeus Laboratoria, Leiden Institute of Chemistry, Einsteinweg 55, P.O Box 9502, 2300 RA Leiden, The Netherlands KEYWORDS. Photosynthesis, electron transfer, nuclear polarization, spin diffusion. 1 ABSTRACT. A sample of solubilized and quinone-depleted reaction centers (RC) from the purple bacterium Rhodobacter (R.) sphaeroides wild-type (WT) has been prepared entirely 13C and 15N isotope labelled at all positions of the protein as well as of the cofactors. In this sample, the occurrence of the solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect has been probed by 13C solid-state magic-angle spinning (MAS) NMR under illumination. Under continuous illumination, signal intensities are modified by the three-spin mixing (TSM) mechanism. Time-resolved illumination experiments reveal the occurrence of light-induced nuclear polarization on the time-scale of hundreds of microseconds, initially dominated by the transient polarization of the singlet branch of the radical-pair mechanism (RPM). A first kinetic analysis shows that the lifetime of the polarization from the singlet branch, indicated by the enhanced absorptive intensities of the signals from aliphatic carbons, is significantly extended.