Lineshape Simulations Research Articles

Heteronuclear relayed E.COSY revisited: determination of 3J(H(alpha),C(gamma)) couplings in Asx and aromatic residues in proteins.

Constant-time 3D heteronuclear relayed E.COSY [Schmidt et al. (1996) J. Biomol. NMR, 7, 142-152], as based on generic 2D small-flip-angle HMQC-COSY [Schmidt et al. (1995) J. Biomol. NMR, 6, 95-105], has been modified to allow for quantitative determination of heteronuclear three-bond 3J(H(alpha),C(gamma)) couplings. The method is applicable to amino acid spin topologies with carbons in the gamma position which lack attached protons, i.e. to asparagine, aspartate, and aromatic residues in uniformly 13C-enriched proteins. The pulse sequence critically exploits heteronuclear triple-quantum coherence (HTQC) of CH2 moieties involving geminal H(beta) proton pairs, taking advantage of improved multiple-quantum relaxation properties, at the same time avoiding scalar couplings between those spins involved in multiple-quantum coherence, thus yielding E.COSY-type multiplets with a splitting structure that is simpler than with the original scheme. Numerical least-squares 2D line-shape simulation is used to extract 3J(H(alpha),C(gamma)) coupling constants which are of relevance to side-chain chi1 dihedral-angle conformations in polypeptides. Methods are demonstrated with recombinant 15N,13C-enriched ribonuclease T1 and Desulfovibrio vulgaris flavodoxin with bound oxidized FMN.

A multinuclear magnetic resonance study of crystalline tripotassium tetracyanocuprate

Direct NMR observation of copper-63/65 nuclei in solid K3Cu(CN)4 provides the first experimental example of anisotropic copper chemical shielding. Axially symmetric by virtue of the space group symmetry, the shielding tensor spans 42 ppm, with the greatest shielding when the unique axis is perpendicular to the applied magnetic field. The nuclear quadrupole coupling constant is also appreciable, CQ(63Cu) = -1.125 MHz, reflecting a deviation of the Cu(CN)43- anion from pure tetrahedral symmetry. Spin-spin coupling to 13C nuclei in an isotopically enriched sample is quantified by line-shape simulations of both 13C and 63/65Cu magic-angle spinning (MAS) NMR spectra to be 300 Hz. It is shown that this information is also directly available by 63/65Cu triple-quantum (3Q) MAS NMR. The relative merits of these three approaches to characterizing spin-spin couplings involving half-integer quadrupolar nuclei are discussed. Chemical shielding tensors for nitrogen-15 and carbon-13 are obtained from NMR spectra of non-spinning samples, and are compared to those of tetrahedral group 12 tetracyanometallates. Finally, 2J(63/65Cu,15N) detected in 15N MAS experiments are found to be 19 and 20 Hz for the two crystallographically distinct cyanide ligands.Key words: NMR, quadrupolar nucleus, chemical shielding tensor, multiple-quantum magic-angle spinning, metal cyanide, spin-spin coupling.

Electron spin resonance studies of defect centers induced in a high-level nuclear waste glass simulant by gamma-irradiation and ion-implantation

Samples of an iron-free soda-lime boro-aluminosilicate high-level nuclear waste (HLW) glass simulant were implantated with 160-keV protons or He + ions or irradiated by 60Co γ-rays. Electron spin resonance (ESR) spectra were recorded before and after implantation or irradiation and after postirradiation isochronal anneals to 550°C. The most numerous paramagnetic states in the unannealed samples following γ-irradiation were boron–oxygen hole centers and Ti 3+ trapped-electron centers. The most numerous paramagnetic states in the as-implanted samples were peroxy radicals (PORs). Annealing of the γ-irradiated samples at temperatures >300°C caused recombination of the trapped electrons and holes, revealing an underlying POR spectrum which annealed in stages at ∼400°C and 550°C, similar to the annealing of PORs in the He +-implanted sample. For equivalent depositions of ionizing energy, the initial POR concentration in the He +-implanted sample was ∼100 times that in the γ-irradiated sample and at least 10 times larger than the (unmeasurable) number of PORs in the proton-implanted sample. Since TRIM calculations indicate that 160-keV protons deliver twice the ionizing dose of He + ions of the same energy but displace only 1/10 as many atoms, it is evident that the PORs induced by He + implantation result from displacements of oxygens in elastic collision cascades. The absence of trapped electrons and holes in the implanted samples is ascribed to annealing during irradiation associated with the fraction of the implantation energy deposited as heat. One of the fundamental defects to be expected in HLW glasses containing α-particle emitters is therefore the POR. Several distinct families of radiation-induced PORs are unambiguously identified in our samples by computer line-shape simulations constrained by the Känzig–Cohen g-value formulae. Possible reasons for the non-observation of PORs in similarly-irradiated glasses containing several wt% Fe 2O 3 are proposed.

Properties of Spin and Fluorescent Labels at a Receptor-Ligand Interface

Site-directed labeling was used to obtain local information on the binding interface in a receptor-ligand complex. As a model we have chosen the specific association of the extracellular part of tissue factor (sTF) and factor VIIa (FVIIa), the primary initiator of the blood coagulation cascade. Different spectroscopic labels were covalently attached to an engineered cysteine in position 140 in sTF, a position normally occupied by a Phe residue previously characterized as an important contributor to the sTF:FVIIa interaction. Two spin labels, IPSL [N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide] and MTSSL [(1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate], and two fluorescent labels, IAEDANS [5-((((2-iodoacetyl)amino) ethyl)amino)naphthalene-1-sulfonic acid] and BADAN [6-bromoacetyl-2-dimethylaminonaphthalene], were used. Spectral data from electron paramagnetic resonance (EPR) and fluorescence spectroscopy showed a substantial change in the local environment of all labels when the sTF:FVIIa complex was formed. However, the interaction was probed differently by each label and these differences in spectral appearance could be attributed to differences in label properties such as size, polarity, and/or flexibility. Accordingly, molecular modeling data suggest that the most favorable orientations are unique for each label. Furthermore, line-shape simulations of EPR spectra and calculations based on fluorescence depolarization measurements provided additional details of the local environment of the labels, thereby confirming a tight protein-protein interaction between FVIIa and sTF when the complex is formed. The tightness of this local interaction is similar to that seen in the interior of globular proteins.

Hydrogen-Bonding Structure of Serine Side Chains in Bombyx mori and Samia cynthia ricini Silk Fibroin Determined by Solid-State 2H NMR

Deuterium solid-state NMR was used to study the dynamics and molecular structure of the serine (Ser) side chains in silk fibroin from Bombyx mori and from Samia cynthia ricini. Samples were selectively labeled with [3,3-2H2]Ser, and the 2H NMR powder spectra were analyzed by line shape simulation. Two types of motion could be characterized quantitatively: one component undergoing a rapid three-site jump (25%) and a second component representing a slow exchange between sites with unequal occupancies and with a small amplitude of libration (75%). From these results, it is concluded that approximately 75% of the Ser residues contribute to the formation of hydrogen bonds in both kinds of silk fibroin from B. mori and S. cynthia ricini. Furthermore, uniaxially oriented silk fibers were used to determine the side-chain conformation and the orientational distribution of the Ser residues in the slow motional component of B. mori silk fibroin. The gauche+ conformer around N−Cα−Cβ−O was found to be dominant, suggesting that the hydroxyl groups of Ser interact with carbonyl groups on adjacent chains and thereby contribute to the intermolecular hydrogen-bonding network of the fiber.

Simulation of excitonic optical line shapes of cyclic molecular aggregates with 9 and 18 units: influence of quasi-static and dynamic disorder

Abstract For Frenkel excitons moving on molecular rings modeling in part bacteria photosynthetic antenna systems we investigate the influence of dynamic and static disorder on their optical line shape. The dynamic disorder, describing the influence of vibrational degrees of freedom, and static disorder are taken into account by fluctuations of the local excitation energies of the BChl molecules. The fluctuations are represented by dichotomic Markov processes with colored noise with different amplitudes and decay constants of the correlation functions. We obtain a closed set of equations of motion for the correlation functions determining the optical line shape which is solved numerically. We display the optical line shapes of the circular aggregates with 9 and 18 BChls for different regimes of the exciton transfer under the influence of the disorders. The line shapes are discussed for various sets of the model parameters describing static and dynamic disorders.

Dynamic properties of P 4O 6S and P 4O 7: [formula omitted] spin–echo and [formula omitted] MAS–NMR investigations

The rotational dynamics of P 4O 6S and P 4O 7 in the solid state were studied by means of 31 P NMR spectra of spinning and static powder samples in the temperature range of 153–295 K and 295–388 K, respectively. All spectra were simulated to confirm the type of the motion and to extract the time scales as a function of the temperature. Good agreement between experimental and theoretical data was obtained on the basis of a three-site jump model. For P 4O 6S, the activation energy and the pre-exponential factor derived from the lineshape simulations amount to 51(2) kJ/mol and 6(3)·10 15 s −1. For P 4O 7, the spectral analysis yields an activation energy of 67(1) kJ/mol and a pre-exponential factor of 6(2)·10 14 s −1. The dynamic behavior was checked independently by lineshape analyses under both MAS and static conditions. Activation energies are consistent within the errors for the lineshape analyses. Additionally, we have analyzed spin–lattice relaxation measurements, which show the correct trends for the activation energies.

Nitroxide Side-Chain Dynamics in a Spin-Labeled Helix-Forming Peptide Revealed by High-Frequency (139.5-GHz) EPR Spectroscopy

High-frequency electron paramagnetic resonance (EPR) spectroscopy has been performed on a nitroxide spin-labeled peptide in fluid aqueous solution. The peptide, which follows the single letter sequence , was reacted with the methanethiosulfonate spin label at the cysteine sulfur. The spin sensitivity of high-frequency EPR is excellent with less than 20 pmol of sample required to obtain spectra with good signal-to-noise ratios. Simulation of the temperature-dependent spectral lineshapes reveals the existence of local anisotropic motion about the nitroxide N–O bond with a motional anisotropy τ⊥/τ∥ (≡ N) approaching 2.6 at 306 K. Comparison with previous work on rigidly labeled peptides suggests that the spin label is reorienting about its side-chain tether. This study demonstrates the feasibility of performing 140-GHz EPR on biological samples in fluid aqueous solution.

Frequency noise spectroscopy lineshape measurements and simulations for a semiconductor laser with strong optical feedback

Semiconductor lasers with strong optical feedback from a plane mirror, or a weakly dispersive diffraction grating, have a frequency noise spectrum that contains a number of noise modes at frequencies close to the modespacing of the external cavity. Experiments and simulations are presented which characterise the measurement of this frequency noise using absorption on an atomic transition. The frequency noise spectroscopy lineshapes are modelled, and characterised experimentally, as a function of the strength of the optical feedback to the semiconductor laser, the detection frequency, the longitudinal mode spacing of the laser system of semiconductor laser and external cavity, the Doppler width of the atomic transition used for detection, and the order of the noise modes. The comparison of simulations and experiment indicate that the measurements behave as expected when the laser system operates in a robust single mode, as determined by optical spectral analysis. The results reinforce the utility of frequency noise spectroscopy as a means of sensitively characterising the output of semiconductor lasers with optical feedback.

Nuclear magnetic resonance line shapes of methyl-like quantum rotors in low-temperature solids

Dissipative dynamics of a tunneling, methyl-like rotor, whose spatial coordinate is weakly coupled to a thermal bath, are described using the reduced density matrix (RDM) approach. It is found that, owing to selection rules imposed on thermally induced transitions by the symmetrization postulate, there are two sorts of coherences between the rotor eigenstates that live long enough to be observed on the nuclear magnetic resonance (NMR) time scale. One comprises degenerate pairs of Kramers sublevels at sequential librational levels of the rotor. The other involves nearly degenerate pairs each of which engages one Kramers sublevel and the remaining sublevel, separated from the Kramers doublet by tunneling quantum. These are the coherences which are seen in the inelastic neutron scattering (INS) patterns of methyl-like rotors. From the RDM equation of motion, augumented with spin-dependent terms relevant in the presence of an external magnetic field, the NMR line shape equation is derived. With no loss of information it can be formulated in terms of only the spin degrees of freedom. Its dissipative part includes two rate constants that describe damping of the long-lived tunneling and Kramers coherences, respectively; coherent tunneling is represented in the Hamiltonian part by an apparent spin-spin coupling. These rate constants are the widths of the inelastic and quasielastic lines, respectively, in the INS spectra of methyl-like rotors; the apparent coupling constant is the shift of the inelastic line. This seems to be the first full exposition of the parallelism between INS and NMR images of tunneling rotors. Rationalization of previous findings involving a CD3 rotor was achieved by use of a simple model of rotor-bath couplings, combined with inferences from numerical simulations of NMR line shapes.

Deuterium NMR Studies of Local Motions of Benzene Adsorbed on Ca-Montmorillonite

2H NMR spectra and interpretations are presented on two samples of deuterium-labeled benzene that have been adsorbed on a major soil component, Ca-montmorillonite clay. Spectra were obtained on the samples with two different benzene loading levels over a wide temperature range and using two values of the quadrupolar echo delay period. Computer simulations of line shapes resulting from various forms of local motion of C−2H moieties provide useful guidelines for interpreting the experimental results. The results suggest that absorbed benzene molecules first form π-complexes with Ca2+ in the interlayer space of the clay with an adsorption enthalpy of 42 ± 4 kJ/mol at temperatures at or below −75 °C. The adsorbed molecules undergo small-angle wobbling of the C6 axis accompanied by rapid discrete jumps about the C6 axis. At higher temperatures, benzene molecules start to perform large-angle wobbling of the C6 axis with extremely fast jumps around the axis, and eventually desorb from Ca2+ to tumble freely in the interlayer space of the clay. The enthalpy and entropy changes between different motional states were obtained from the variable temperature studies. The activation energies of relevant molecular motions were also estimated. This approach is attractive for elucidation of the detailed motional behaviors of organic pollutants adsorbed in soil.

Three-body interaction-induced light scattering in krypton gas: a computer simulation of the spectral line shapes

The two-, three- and four-body effective collision induced scattering spectral line shapes are calculated for dense gaseous krypton using the pairwise additivity (PA) approximation and different polarizability models. These spectra and several interaction induced spectra calculated at various densities are compared with the experimental measurements of Barocchi et al. [1988, Europhys. Lett., 5, 607]. The potential effect on the spectrum is found to be weak. The results obtained with the Meinander et al. [1986, J. chem. Phys., 84, 3005] empirical polarizability model and molecular dynamics fit well the experimental two- and three-body spectral shapes. The irreducible contribution to the spectral shape is evaluated using the dipole induced dipole irreducible polarizability [buckingham, A. D., and Hands, I. D., 1991, Chem. Phys. Lett., 185, 544]. This contribution is found to be relatively weak for the anisotropic spectra in the frequency and density range studied, explaining the good agreement between the pairwise approximation calculations and the experimental data. The spectra radiated by the quasi-molecules Kr2, Kr3, and Kr4 (the total spectrum within the PA approximation) are also simulated.

Three-body interaction-induced light scattering in krypton gas: a computer simulation of the spectral line shapes

The two-, three- and four-body effective collision induced scattering spectral line shapes are calculated for dense gaseous krypton using the pairwise additivity (PA) approximation and different polarizability models. These spectra and several interaction induced spectra calculated at various densities are compared with the experimental measurements of Barocchi et al. [1988, Europhys. Lett., 5, 607]. The potential effect on the spectrum is found to be weak. The results obtained with the Meinander et al. [1986, J. chem. Phys., 84, 3005] empirical polarizability model and molecular dynamics fit well the experimental two- and three-body spectral shapes. The irreducible contribution to the spectral shape is evaluated using the dipole induced dipole irreducible polarizability [buckingham, A. D., and Hands, I. D., 1991, Chem. Phys. Lett., 185, 544]. This contribution is found to be relatively weak for the anisotropic spectra in the frequency and density range studied, explaining the good agreement between the pairwise approximation calculations and the experimental data. The spectra radiated by the quasi-molecules Kr2, Kr3, and Kr4 (the total spectrum within the PA approximation) are also simulated.

Simulation of Magnetic Resonance Static Powder Lineshapes: A Quantitative Assessment of Spherical Codes

Simulation of magnetic resonance static powder spectra is performed by a (possibly weighted) summation of single-crystal spectra computed for different orientations of the external field with respect to the principal axes of the magnetic interactions. The many available methods differ in the choice of the integration points (i.e., orientations) and weights, the set of which is called spherical code. There is continuing interest in minimizing the number of integration points necessary to a good simulation. Neglecting the possible interpolation of transition frequencies and intensities between integration points, we turn our attention to the efficiency of spherical codes themselves. To this end, an unbiased quantitative procedure to assess their efficiency in simulating magnetic resonance static powder spectra is proposed. To achieve an impartial judgement, the procedure has been designed by carefully taking into consideration the following points: choice of exact reference spectra; accurate definition of the merit figures; extended range of number of integration points; orientation dependence of the efficiency. The proposed procedure has been applied to an inclusive set of 23 spherical codes. It was found that most codes perform rather similarly. SPIRAL is the most efficient code, whereas Monte Carlo and “repulsive” codes show the best rotational invariance of the simulated lineshape with respect to the orientation of the spherical code.

Local Motions of Organic Pollutants in Soil Components, as Studied by 2H NMR

2H NMR spectra and interpretations are presented on a series of samples, each consisting of a deuterium-labeled organic pollutant (trichloroethylene, acetone, pyridine, benzene, or ethylene glycol) adsorbed on a soil component (montmorillonite clay or humic acid). Spectra were obtained over a wide temperature range and using two values of the quadrupolar echo delay period. Computer simulations of line shapes resulting from various forms of local motion of C−2H moieties provide useful guidelines for interpreting the experimental results. In a few cases, detailed line shape simulations are given. This approach is attractive for elucidation of the detailed motional behaviors of organic pollutants adsorbed in soil.

Simulation of one-dimensional magnetic resonance powder lineshapes reduced to area computation

Up to now, computation of magnetic resonance powder lineshapes has been performed by summing single-crystal spectra computed at different orientations. In this Letter, a novel method to compute one-dimensional magnetic resonance powder spectra from experiments with axially symmetric setup is proposed. It is based on an adaptive interpolation technique requiring the calculation of contours of constant transition frequency (and constant line amplitude) and of the area of the regions enclosed by such contours. The method is given mathematical justification, is implemented in a computer program, and its efficiency is compared with that of existing methods. Extension to multi-dimensional spectra and to experiments with non-axial setup is briefly discussed.

The Alignment of Lyotropic Liquid Crystals Formed by Hexadecyltrimethylammonium Bromide in D2O in a Magnetic Field

The alignment of lyotropic liquid crystals formed by hexadecyltrimethylammonium bromide (CTAB, where C stands for cetyl) with D2O was studied by the use of 2H NMR. At CTAB/D2O concentrations between 1.01 and 1.29 mol/kg, liquid crystal domains aligned in the magnetic field within a few hours. The dependence of the characteristic alignment time on concentration and temperature has been determined. At higher concentrations, no alignment took place due to the high viscosity of the system. At lower concentrations, the alignment could not be observed by 2H NMR. The addition of sodium salicylate (NaSal), at equal molar concentrations of CTAB and NaSal, changed the orientation of the micelles from parallel to the magnetic field to perpendicular to the field. Line-shape simulations were carried out to give estimates on the rate of exchange between free D2O molecules and those bounded to the micelles, as well as on the deuterium quadrupole splittings for D2O molecules bound to micelles. The dependence of the characteristic alignment time on the strength of magnetic field was also studied.

Rotationally induced triple quantum coherence excitation in MAS NMR spectroscopy of I=5/2 spins

Rotationally induced excitation of triple quantum coherences is demonstrated unequivocally for I=5/2 nuclei from comparison of the variation of the observed and simulated lineshapes as a function of spin-lock time. A new pulse sequence is presented that produces purely absorptive lineshapes from such an experiment. An important observation is that the coherence transfer goes through a maximum at moderate rf fields.

Out-of-Plane Motion of the Guest Benzene Molecule Trapped in a [Cd(dmen)2(CN)]2[Cd(CN)4] Host as Studied by 2H-NMR

An out-of-plane rotational motion of the guest benzene molecule trapped in a [Cd(dmen)2(CN)]2[Cd(CN)4] host, which is a cadmium cyano complex (dmen = N,N'-dimethyl-1,2-diaminoethane), was detected by means of 2H-NMR powder patterns measured over a temperature range of 123–423 K. A simple inequivalent 8-site reorientation model which has two independent populations was used in the line shape simulation, and the potential trapping the benzene molecule was analyzed to be transformable depending on temperature. Structural flexibility of the host, which is considered to be a cause of the variable potential, was confirmed from the detection of a puckering-like motion of the dmen chelate ring that makes a part of the inner wall of the cavity trapping the guest benzene molecule.

On the consequences of a realistic conditional covariance in MMM-calculations

The model microfield method (MMM) may be used to include the effect of ion motion in line shape calculations. This kind of modelling of the time evolution of the microfield as a stochastic process, as is done in this method, yields a short time behaviour of the conditional covariance of the model microfield, which differs considerably from a conditional covariance calculated by considering the real motion of the plasma ions (microscopic conditional covariance). In this work purely ionic broadened hydrogen profiles are calculated using the microscopic conditional covariance within the MMM. It is shown that, depending on the reduced radiator-perturber mass, these MMM calculations may lead to unphysical line shapes. For comparison, hydrogen profiles derived within the MMM using the kangaroo process and from line shape simulations are given.