Explanation of spin-lattice relaxation rates of spin labels obtained with multifrequency saturation recovery EPR

Electron paramagnetic resonance (EPR) pulsed saturation recovery (pSR) measurements of spin-lattice relaxation rates have been made on nitroxide-containing fatty acids embedded in lipid bilayers by Hyde and co-workers. The data have been collected for a number of spin-labeled fatty acids at several microwave spectrometer frequencies (from 2 to 35 GHz). We compare these spin-lattice relaxation rates to those predicted by the Redfield theory incorporating several mechanisms. The dominant relaxation mechanism at low spectrometer frequencies is the electron-nuclear dipolar (END) process, with spin rotation (SR), chemical shift anisotropy (CSA), and a generalized spin diffusion (GSD) mechanism all contributing. The use of a wide range of spectrometer frequencies makes clear that the dynamics cannot be modeled adequately by rigid-body isotropic rotational motion. The dynamics of rigid-body anisotropic rotational motion is sufficient to explain the experimental relaxation rates within the experimental error. More refined models of the motion could have been considered, and our analysis does not rule them out. However, the results demonstrate that measurements at only two suitably chosen spectrometer frequencies are sufficient to distinguish anisotropic from isotropic motion. The results presented demonstrate that the principal mechanisms responsible for anisotropically driven spin-lattice relaxation are well understood in the liquids regime.     

Cross-correlated relaxation between H1' chemical shift anisotropy and H1'-H2' dipolar relaxation mechanisms in ribonucleosides: application to the characterization of their anomeric configuration

Cross-correlated nuclear spin relaxation between 1H chemical shift anisotropy (CSA) and 1H-1H dipolar relaxation mechanisms in ribonucleosides in solution phase are observed and used to identify their anomeric configuration. Only alpha-ribonucleosides showed the presence of cross-correlated spin relaxation through differential spin-lattice relaxation (T1) of the H1' doublet. Dependence of the magnitude and the orientation of the H1' CSA tensor values on the glycosidic torsion angle and the fast time-scale internal motions present in the ribose moiety play a significant role in the characterization of the anomeric configuration of the nucleosides via cross-correlated relaxation.     

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.     

Theoretical aspects of chemically induced magnetic polarization

The role of theory in guiding and simplifying interpretation of electron spin resonance experiments on photochemical and other reactions involving free radical intermediates is surveyed. Emphasis is on models which provide a physical picture as well as quantitative estimates for such phenomena as the radical pair mechanism of chemically induced electron spin polarization (CIDEP), the closely related process of spin exchange during radical-radical encounters, and spin lattice relaxation. Some specific topics discussed are: 1) an improved quantitative model of STo CIDEP combining an initial stage of polarization development followed partial loss of this polarization to spin exchange, 2) the relation between the spin exchange and recombination rate constants, and 3) simplification of spin-lattice relaxation in the common case of spin-rotation relaxation. The modification of the polarization processes in two-dimensional and closed three-dimensional systems is also discussed     

Conformational flexibility of DNA

Pulsed Electron-Electron Double Resonance (PELDOR) on double-stranded DNA (ds-DNA) was used to investigate the conformational flexibility of helical DNA. Stretching, twisting, and bending flexibility of ds-DNA was determined by incorporation of two rigid nitroxide spin labels into a series of 20 base pair (bp) DNA duplexes. Orientation-selective PELDOR experiments performed at both X-band (9 GHz/0.3 T) and G-band (180 GHz/6.4 T) with spin label distances in the range of 2-4 nm allowed us to differentiate between different simple models of DNA dynamics existing in the literature. All of our experimental results are in full agreement with a dynamic model for ds-DNA molecules, where stretching of the molecule leads to a slightly reduced radius of the helix induced by a cooperative twist-stretch coupling.     

Cytosine methylation regulates DNA bendability depending on the curvature

Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, i.e., a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.

D-shaped DNA is used to observe dsDNA bending mechanics. Cytosine methylation increases the intrinsic stiffness of dsDNA. Under strong bending, methylation stabilizes or destabilizes a kink form depending on methylation sites.     

Relative molecular weight distributions of cis-polybenzoxazole/polyphosphoric acid rodlike liquid crystalline polymer solutions from dilute solution rheometry

The molecular weight for a dilute solution of cis-polybenzoxazole (PBO) in polyphosphoric acid (PPA) was determined by fitting the rheological data with a semiempirical polydisperse hybrid theory. The hybrid theory models a semiflexible rigid rod as an elastic cylinder. The cylinder has both a rotational relaxation spectrum given by an ideal rigid rod and an internal bending relaxation spectrum spaced in accord with the relaxation time spectra of a flexible coil with fully developed hydrodynamic interactions. The model was fitted to rheological data collected for a 0.05 weight percent solution with intrinsic velocity (one-point determination) of 320 ± 10 cc/g. The model predicts a number-average molecular weight near 12800 ± 400 g/mol with a polydispersity index of 2.5 ± 0.1. By using the Yamakawa-Yoshizaki equation the intrinsic viscosity is calculated for the model molecular weight distribution as 310 cc/g.     

Molecular properties determined from the relaxation of long-lived spin states

The populations of long-lived spin states, in particular, populations of singlet states that are comprised of antisymmetric combinations of product states, |alpha(I)beta(S)> - |beta(I)alpha(S)>, are characterized by very long lifetimes because the dipole-dipole interaction between the two "active" spins I and S that are involved in such states is inoperative as a relaxation mechanism. The relaxation rate constants of long-lived (singlet) states are therefore determined by the chemical shift anisotropy (CSA) of the active spins and by dipole-dipole interactions with passive spins. For a pair of coupled spins, the singlet-state relaxation rate constants strongly depend on the magnitudes and orientations of the CSA tensors. The relaxation properties of long-lived states therefore reveal new information about molecular symmetry and structure and about spectral density functions that characterize the dynamic behavior.     

Magnetic relaxation dispersion of lithium ion in solutions of DNA

The magnetic field dependence of the nuclear spin-lattice relaxation rate constant defines the magnetic relaxation dispersion (MRD) and provides a direct characterization of the molecular dynamics that cause fluctuations in the magnetic couplings in the system and may also indicate the dimensional constraints on the motion. The counterion cloud surrounding a linear polyelectrolyte ion, such as DNA in solution, provides an interesting opportunity for ion confinement that helps in understanding the thermodynamics and the dynamics of the interactions between the polyion and other solutes. The MRD profiles of lithium ion and tetramethylammonium ion were recorded in dilute aqueous solutions of native calf thymus DNA, which provides a long, charged rod that reorients slowly. The 7Li ion relaxes through the nuclear electric quadrupole coupling and the proton-lithium dipole-dipole coupling; the protons of the tetramethylammonium ion relax by dipole-dipole coupling. MRD profiles of the 7Li+ ion are dominated by transient interactions with the DNA that yield a linear dependence of the spin-lattice relaxation rate constant on the logarithm of the Larmor frequency. This magnetic field dependence is consistent with diffusive ion motions that modulate two spatial coordinates that characterize the relaxation couplings in the vicinity of the polyion. Motions around the rod and fluctuations in the ion distance from the rod are consistent with these constraints for lithium. The magnetic field dependence of the tetramethylammonium ion proton relaxation rate constant is weak, but also approximately a linear function of the logarithm of the Larmor frequency, which implies that the field dependence is caused in part by local order in the DNA solution.     

Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase

We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET) techniques to study the interaction between EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution. Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip out the second adenine for methylation. The binding affinity of M.EcoRI to two dsDNA fragments (20 and 38 bp) was studied with fluorescence anisotropy. Their binding constants at different temperatures from 20 to 40 degrees C were obtained, and the thermodynamic parameters of binding were derived. The results showed that M.EcoRI had a higher binding affinity to the short dsDNA strand than to the long one, and its binding to DNA was primarily entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we were able to monitor the enhanced TMR fluorescence in the presence of M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET efficiency was changed from 72.4 to 63.4 A, and the DNA bending angle was estimated as 57.8 degrees .     

SOLID-STATE HIGH RESOLUTION NMR STUDY ON POLY (2, 6-DIMETHYL-1,4-PHENYLENE OXIDE)

Experiments including ~(13)C spin-lattice relaxation, ~(13)C heteronuclear dipolar dephasing and~1H spin diffusion are performed on poly (2, 6-dimethyl-1, 4-phenylene oxide) (PPO). Theresults show that the rotation of the methyl groups in solid PPO is partially restricted, whichresults in a surprisingly efficient spin diffusion between the aromatic proton and methyl protoncharacterized by a diffusion time of 150μs. The results also show that the aromatic ring insolid PPO is rigid and twisted, which causes all aromatic carbons to be chemicallyunequivalent.     

Furanose dynamics in the HhaI methyltransferase target DNA studied by solution and solid-state NMR relaxation

Both solid-state and solution NMR relaxation measurements are routinely used to quantify the internal dynamics of biomolecules, but in very few cases have these two techniques been applied to the same system, and even fewer attempts have been made so far to describe the results obtained through these two methods through a common theoretical framework. We have previously collected both solution 13C and solid-state 2H relaxation measurements for multiple nuclei within the furanose rings of several nucleotides of the DNA sequence recognized by HhaI methyltransferase. The data demonstrated that the furanose rings within the GCGC recognition sequence are very flexible, with the furanose rings of the cytidine, which is the methylation target, experiencing the most extensive motions. To interpret these experimental results quantitatively, we have developed a dynamic model of furanose rings based on the analysis of solid-state 2H line shapes. The motions are modeled by treating bond reorientations as Brownian excursions within a restoring potential. By applying this model, we are able to reproduce the rates of 2H spin-lattice relaxation in the solid and 13C spin-lattice relaxation in solution using comparable restoring force constants and internal diffusion coefficients. As expected, the 13C relaxation rates in solution are less sensitive to motions that are slower than overall molecular tumbling than to the details of global molecular reorientation, but are somewhat more sensitive to motions in the immediate region of the Larmor frequency. Thus, we conclude that the local internal motions of this DNA oligomer in solution and in the hydrated solid state are virtually the same, and we validate an approach to the conjoint analysis of solution and solid-state NMR relaxation and line shapes data, with wide applicability to many biophysical problems.     

Rotational and translational relaxation times of quasi-elastic and rigid dumbbells elastically bound to polymer network junctions

The dynamics of a rigid rod located between fixed junctions of a polymer network is studied. Three approaches are used in the solution of this problem. The first is based on the viscoelastic model, where a rigid rod is simulated by an elastic dumbbell with a fixed average length; the second includes solution of equations of motion for projections of the rigid rod using the Lagrangian multipliers under the constraint condition; and the third involves solution of the diffusion equation in the presence of an elastic potential. The second and third approaches allow calculation of orientational relaxation times for rod projections under the action of a strong orienting field. The dependences of the relaxation times of orientational and translational motions of the rod projections on the coordinate axes and the orientational relaxation times of mean-square rod projections on the model parameters (the distances between fixed polymer network junctions, the length of the rigid rod, and the elastic coefficient characterizing the binding between the rod and the network) are found.     

Low-field approach to double resonance in nuclear quadrupole resonance of spin-1 nuclei

Using double-resonance conditions, in which the Larmor frequency of a spin-1/2 nucleus is matched to one of the nuclear quadrupole resonance frequencies of a spin-1 nucleus, the authors demonstrate increased cross relaxation between the two nuclear spin species. They calculate the cross-relaxation rate using the motionally averaged heterogeneous dipole Hamiltonian as a perturbation to the combined quadrupole and Zeeman Hamiltonians. Using this cross-relaxation rate, in addition to hydrogen and nitrogen autorelaxation rates, expressions governing spin-1/2 and spin-1 spin-lattice relaxation are determined. With ammonium nitrate, containing nitrogen (spin-1) and hydrogen (spin-1/2), increased nitrogen signal and spin-lattice relaxation are demonstrated, using fields less than 120 G. The cross-relaxation rate is also measured and an overall signal/noise improvement by a factor of 2.3+/-0.1 is attained.     

Pressure effects on the electron spin relaxation of several radicals in solution

The pressure effect on the decay rate of chemically induced dynamic electron spin polarization (CIDEP) was investigated on several free-radical intermediates in photolysis, and the spin-lattice relaxation times for these radicals were estimated from the decay rates of CIDEP signals at various pressures. The spin-lattice relaxation rates were retarded by increasing external pressure. From the pressure dependence of the spin-lattice relaxation rates the activation volume was estimated. The activation volumes of these radicals divide into two groups; ≈30 cm³ mol⁻¹ for negative ions and ≈10 cm³ mol⁻¹ for neutral radicals.     

Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove

The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.     

Chemistry of the phenoxathiins and isosterically related heterocycles. XXIII . 1-azathianthrene: First reported synthesis of a monoazathianthrene and the investigation of the 13C-NMR spectrum using two-dimensional NMR techniques

The reaction of the dianion of 3-mercaptopyridin-2(1H)-thione with 2-chloronitrobenzene in N,N-dimethylformamide leads to the formation of 1-azathianthrene, the first reported mono-aza analog of the thianthrene ring system. A partial assignment of the ¹³C-nmr spectrum of the title compound is reported, the assignment based on chemical shift arguments, spin-lattice (T₁) relaxation times and ¹H-¹³C spin coupling constants. Amplitude modulated two-dimensional Fourier transform (AM2DFT) techniques were employed for the acquisition of the heteronuclear spin-coupling constants.     

High field 207Pb spin-lattice relaxation in solid lead nitrate and lead molybdate

Spin-lattice relaxation rates of lead have been measured at 17.6 T (156.9 MHz) as a function of temperature in polycrystalline lead nitrate and lead molybdate. Comparing the results with relaxation rates measured at lower fields, it is found that at high fields and low temperature, chemical shift anisotropy (CSA) makes small but observable contributions to lead relaxation in both materials. At 17.6 T and 200 K, CSA accounts for about 15% of the observed relaxation rate. Above 300 K, the dominant relaxation mechanism even at 17.6 T is an indirect Raman process involving modulation of the (207)Pb spin-rotation tensor, as first proposed by Grutzner et al. [J. Am. Chem. Soc. 123, 7094 (2001)] and later treated theoretically in more detail by Vega et al. [Phys. Rev. B 74, 214420 (2006)]. The improved signal to noise ratio at high fields makes it possible to quantify relaxation time anisotropy by analyzing saturation-recovery functions for individual frequencies on the powder pattern line shape. No orientation dependence is found for the spin-lattice relaxation rate of either material. It is argued from examination of the appropriate theoretical expressions, derived here for the first time, that the lack of observable relaxation time anisotropy is probably a general feature of this indirect Raman mechanism.     

Importance of the O-M-O bridges (M = V5+, Mo6+) for the spin-exchange interactions in the magnetic oxides of Cu2+ ions bridged by MO4 tetrahedra: spin-lattice models of Rb2Cu2(MoO4)3, BaCu2V2O8, and KBa3Ca4Cu3V7O28

The spin-lattice models relevant for the magnetic oxides Rb2Cu2(MoO4)3, BaCu2V2O8, and KBa3Ca4Cu3V7O28 were determined by evaluating the relative strengths of the spin-exchange interactions between their Cu2+ ions on the basis of spin dimer analysis. Our study shows that the O-M-O bridges (M = V5+, Mo6+) between the magnetic ions Cu2+, provided by the MO4 tetrahedra, are crucial for the spin-exchange interactions and hence for deducing the spin-lattice models needed to interpret the magnetic properties of these oxides. The spin-lattice model of Rb2Cu2(MoO4)3 is not a uniform chain but two interpenetrating spin ladders that interact weakly with geometric spin frustration. The spin-lattice model of BaCu2V2O8 is an alternating chain as expected, but the spin-exchange paths responsible for it differ from those expected. With respect to the strongest spin exchange of BaCu2V2O8, the spin exchange of KBa3Ca4Cu3V7O28 is only slightly weaker, but the strongest spin exchange of Rb2Cu2(MoO4)3 is much weaker. This difference in the spin-exchange strengths is caused by the difference in the bridging modes of the MO4 tetrahedra leading to these spin-exchange interactions.