Lineshape Simulations Research Articles

Molecular dynamics simulation of NMR powder lineshapes of linear guests in structure I clathrate hydrates

We perform molecular dynamics simulations (up to 6 ns) for the structure I clathrate hydrates of linear molecules CS, CS(2), OCS, and C(2)H(2) in large cages at different temperatures in the stability range to determine the angular distribution and dynamics of the guests in the large cages. The long axes of linear guest molecules in the oblate large structure I clathrate hydrate cages are primarily confined near the equatorial plane of the cage rather than axial regions. This non-uniform spatial distribution leads to well-known anisotropic lineshapes in the solid-state NMR spectra of the guest species. We use the dynamic distribution of guest orientations in the cages during the MD simulations at different temperatures to predict the (13)C NMR powder lineshapes of the guests in the large cages. The length of the guests and intermolecular interactions of the guests in the water cages determine the angular distribution and the mobility of the guests in the sI large cages at different temperatures. At low temperatures the range of motion of the guests in the cages are limited and this is reflected in the skew of the predicted (13)C lineshapes. As the guest molecules reach the fast motion limit at higher temperatures, the lineshapes for CS, OCS, and C(2)H(2) are predicted to have the "standard" powder lineshapes of guest molecules.

基于一维辐射转移方程的等离子体发射谱线线形模拟

基于一维辐射转移方程的等离子体发射谱线线形模拟

Lattice defect assisted incorporation of Mn2+ ions in cubic II-VI semiconductor quantum dots

Electron paramagnetic resonance spectra from substitutional Mn2+ ions in quantum dots of cubic ZnS with tight size distribution centred at 2 nm were recorded in the 9.8 GHz and 34 GHz frequency bands. Their quantitative analysis with line shape simulation and fitting computer programs accounting for both forbidden transitions and line broadening effects demonstrate the presence of a local axial distortion attributed to a neighbouring extended planar stacking defect. The presence of such extended lattice defects, confirmed from a high resolution transmission electron microscopy study on presently investigated cubic ZnS quantum dots, seems to be essential in the incorporation and localization of Mn2+ activating ions in other cubic II-VI semiconductor quantum dots as well.

ChemInform Abstract: Radical Cations of cis- and trans-1,3-Di- and 1,3,5- Trimethylcyclohexanes. Matrix Influence on Two Nearly Degenerate SOMOs

Radical cations of cis and trans isomers of 1,3-di- and 1,3,5-tri-methylcyclohexane, stabilized in various γ-irradiated solute–halocarbon matrices at 77 K and above, have been investigated by means of EPR spectroscopy. The hfs constants have been compared with those calculated using semiempirical methods, INDO (spin density) and MNDO (geometry optimizations). The SOMOs of the methyl-substituted cyclohexane cations are all similar to either of the orbitals, ag or bg, following a Jahn–Teller split of the eg orbital (HOMO) of cyclohexane. The selection of SOMO depends on matrix and isomer. The trans isomers have one axial methyl group and the cations were found to take an ag-like SOMO in all matrices used, with large spin density on the equatorial hydrogen attached to the axially substituted ring-carbon. Using CF3CCl3 as matrix the EPR signal due to the trans-1,3,5-trimethylcyclohexane cation contains (in addition) a spectrum of the bg-like SOMO superimposed. The cation of cis-1,3-dimethylcyclohexane shows contributions from both SOMOs in the matrices CF3-cC6F11, CF2ClCFCl2 and CF3CCl3, but exclusively a bg-like SOMO in cC6F12. A bg-like SOMO is observed for the cis-1,3,5-trimethylcyclohexane cation in all matrices. The abundance ratios, [ag]/[bg], for the cases where the matrix-stabilized cation shows contribution from both bg- and ag-like SOMOs simultaneously, are found to be ca. 1/4 from line shape simulations. No prominent temperature dependence of this ratio is detected.

Ring inversion process for a series of 3,5-dialkyl-1-oxa-3,5-diazacyclohexanes: 1H DNMR study and semiempirical calculations

The ring inversion process for a series of 3,5-dialkyl-1-oxa-3,5-diazacyclohexanes was studied using proton dynamic nuclear magnetic resonance (1H DNMR) spectroscopy in conjunction with semiempirical calculations. At low temperature, the ring methylene protons decoalesced into two AB spin systems in a 2:1 ratio. Lineshape simulations of the DNMR spectra provided first-order rate constants for magnetic exchange. The energy barrier for each inversion reaction was calculated from the respective rate constants. In general, as the size of the N-alkyl group increased, the barrier to ring inversion decreased. A similar trend was seen in semiempirical calculations that modeled the ring inversion process. Copyright © 2010 John Wiley & Sons, Ltd.

Trading sensitivity for information: Carr–Purcell–Meiboom–Gill acquisition in solid-state NMR

The Carr-Purcell-Meiboom-Gill (CPMG) experiment has gained popularity in solid-state NMR as a method for enhancing sensitivity for anisotropically broadened spectra of both spin 1/2 and half integer quadrupolar nuclei. Most commonly, the train of CPMG echoes is Fourier transformed directly, which causes the NMR powder pattern to break up into a series of sidebands, sometimes called "spikelets." Larger sensitivity enhancements are observed as the delay between the pi pulses is shortened. As the duration between the pi pulses is shortened, however, the echoes become truncated and information about the nuclear spin interactions is lost. We explored the relationship between enhanced sensitivity and loss of information as a function of the product Omega 2tau, where Omega is the span of the anisotropic lineshape and 2tau is the pi pulse spacing. For a lineshape dominated by the nuclear shielding anisotropy, we found that the minimum uncertainty in the tensor values is obtained using Omega 2tau values in the range Omega 2tau approximately 12(-1)(+6) and Omega 2tau approximately 9(-3)(+3) for eta(s)=0 and eta(s)=1, respectively. For an anisotropic second-order quadrupolar central transition lineshape under magic-angle spinning (MAS), the optimum range of Omega 2tau approximately 9(-2)(+3) was found. Additionally, we show how the Two-dimensional One Pulse (TOP) like processing approach can be used to eliminate the cumbersome sideband pattern lineshape and recover a more familiar lineshape that is easily analyzed with conventional lineshape simulation algorithms.

45Sc Solid State NMR Spectroscopy – A Complementary Tool to X‐ray Crystallography for Structure Determination of Intermetallic Compounds

Abstract45Sc solid state NMR spectroscopy is a useful complementary tool to X‐ray crystallography for structure determination. Recent developments in the field of intermetallic scandium compounds are reviewed. The structural topics concern defect formation, structural disorder, superstructure formation, as well as the detection of multiple scandium sites. To address questions of this kind, high‐resolution 45Sc NMR spectroscopic techniques were established as a new structural tool for the quantification of the local coordination scandium environments and the detailed characterization of their internal NMR interaction parameters. Owing to the moderately sized nuclear electric quadrupole moment of 45Sc, the magic‐angle spinning spectra are affected both by first‐ and second‐order quadrupolar perturbations, which can be analyzed and quantified by fast magic angle spinning, assisted by lineshape simulations. The resolution can be further improved by correlating triple quantum (TQ) with single quantum coherences. Using this 2D NMR spectroscopic methodology, the effects of magnetic shielding and second‐order quadrupolar perturbations on the MAS NMR lineshape can be separated, enabling a more precise experimental characterization of electric field gradients present at the 45Sc nuclei. Structure validation includes the precise measurement of these parameters and comparison with quantum mechanically calculated values based on the atomic positions. In this regard, satisfactory results were obtained using the WIEN2k program.

Electronic structure of the primary electron donor of Blastochloris viridis heterodimer mutants: High-field EPR study

High-field electron paramagnetic resonance (HF EPR) has been employed to investigate the primary electron donor electronic structure of Blastochloris viridis heterodimer mutant reaction centers (RCs). In these mutants the amino acid substitution His(M200)Leu or His(L173)Leu eliminates a ligand to the primary electron donor, resulting in the loss of a magnesium in one of the constituent bacteriochlorophylls (BChl). Thus, the native BChl/BChl homodimer primary donor is converted into a BChl/bacteriopheophytin (BPhe) heterodimer. The heterodimer primary donor radical in chemically oxidized RCs exhibits a broadened EPR line indicating a highly asymmetric distribution of the unpaired electron over both dimer constituents. Observed triplet state EPR signals confirm localization of the excitation on the BChl half of the heterodimer primary donor. Theoretical simulation of the triplet EPR lineshapes clearly shows that, in the case of mutants, triplet states are formed by an intersystem crossing mechanism in contrast to the radical pair mechanism in wild type RCs. Photooxidation of the mutant RCs results in formation of a BPhe anion radical within the heterodimer pair. The accumulation of an intradimer BPhe anion is caused by the substantial loss of interaction between constituents of the heterodimer primary donor along with an increase in the reduction potential of the heterodimer primary donor D/D + couple. This allows oxidation of the cytochrome even at cryogenic temperatures and reduction of each constituent of the heterodimer primary donor individually. Despite a low yield of primary donor radicals, the enhancement of the semiquinone–iron pair EPR signals in these mutants indicates the presence of kinetically viable electron donors.

Computer Simulation of the Deuterium NMR Spectra Reflecting the Director Distribution for Multi-Domains in a Thin Nematic Cell

Deuterium NMR spectroscopy is widely employed to investigate the static and dynamic director alignment for low molar mass nematics contained in a thin sandwich cell. When the director is not uniformly aligned the appearance of the deuterium NMR spectra, recorded in the measurements, reflects the form of the director distribution. This occurs because the observed spectrum is a weighted sum of the spectra from all director orientations in the sample. In order to obtain the form of the director distribution function by simulating the spectra it is necessary to know how the spectral lineshape varys with the director orientation. As well as being of practical relevance, when the director distributes thermally with the average director orientation in multi domains, this contribution to the lineshape is of fundamental interest for nematic behaviour. Here we explore ways to vary the aveage director orientation using an electric field and employ this to measure the voltage dependence of the NMR lineshapes for the nematic phase of 5CB-d2. This approach is investigated by using a computer simulation of the NMR lineshapes.

Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra

We have carried out a comparative study of five ab initio electrostatic frequency maps and a semiempirical model for the amide-I and -II modes. Unrestrained molecular dynamics simulation of a 3(10)-helical peptide, Z-Aib-L-Leu-(Aib)(2)-Gly-OtBu, in CDCl(3) is performed using the AMBER ff99SB force field, and the linear and two-dimensional infrared (2D IR) spectra are simulated on the basis of a vibrational exciton Hamiltonian model. A new electrostatic potential-based amide-I and -II frequency map for N-methylacetamide is developed in this study. This map and other maps developed by different research groups are applied to calculate the local mode frequencies of the amide linkages in the hexapeptide. The simulated amide-I line shape from all models agrees well with the previous experimental results on the same system, except for an overall frequency shift. In contrast, the simulated amide-II bands are more sensitive to the frequency maps. Essential features obtained in the electrostatic models are captured by the semiempirical model that takes into account only the intramolecular hydrogen bonding effects and solvent shifts. Detailed comparisons between the models are also drawn through analysis of the local mode frequency shifts. Among all of the maps tested in this study, the new four-site potential map performs quite well in simulating the amide-II bands. It properly predicts the effects of hydrogen bonding on the amide-I and -II frequencies and reasonably simulates the isotope-dependent amide-I/II cross peaks upon (13)C=(18)O/(15)N substitutions.

Relation between Theories, Experiments, and Simulations of Spectral Line Shapes

Simulations of Shapes and Shifts of Spectral Lines (SSSL) are important as the third powerful research methodology—in addition to theories and experiments. However, there is a growing tendency in physics in general and in the area of SSSL in particular, to consider the ultimate test of any theory to be the comparison with results of a code based on fully-numerical simulations starting from the “scratch” rather than from some analytical advance. In this paper, we show by examples that fully-numerical simulations are often not properly verified and validated, fail to capture emergent principles and phenomena, and lack the physical insight. Physics is the experimental science. So, the ultimate test of any theory—including theories of SSSL—should be the comparison with experiments conducted in well-controlled conditions (benchmark experiments).

Oxygen Transport in Sc-Doped CeO2: Cation (45Sc) NMR as a Probe of Anionic Conductivity

Oxygen-vacancy hopping dynamics in Sc-doped CeO2, a solid electrolyte (SE), was studied employing high-temperature (up to 600 °C) 45Sc nuclear magnetic resonance (NMR) and electrochemical impedance spectroscopy (EIS) techniques. The oxygen-vacancy hopping frequency and its temperature dependence, as obtained from the simulation of 45Sc NMR line shapes, are in excellent agreement with those obtained from EIS. The characteristic length scale of the vacancy hopping is found to be controlled by the average Sc−Sc separation in the lattice. Moreover, direct spectroscopic evidence for the presence of small but significant dynamical heterogeneities is observed, implying that all vacancies are not characterized by similar dynamic properties. These results clearly demonstrate that cation NMR can serve as a unique probe for anionic transport in SEs.

Electron spin resonance in membrane research: protein-lipid interactions from challenging beginnings to state of the art.

Conventional electron paramagnetic resonance (EPR) spectra of lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid–protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, and 7 distinct species of lipids. Lineshape simulations of the two-component conventional spin-label EPR spectra allow estimation of the rate at which protein-associated lipids exchange with those in the bulk fluid regions of the membrane. For lipids that do not display a selectivity for the protein, the intrinsic off-rates for exchange are in the region of 10 MHz: less than 10× slower than the rates of diffusive exchange in fluid lipid membranes. Lipids with an affinity for the protein, relative to the background lipid, have off-rates for leaving the protein that are correspondingly slower. Non-linear EPR, which depends on saturation of the spectrum at high radiation intensities, is optimally sensitive to dynamics on the timescale of spin-lattice relaxation, i.e., the microsecond regime. Both progressive saturation and saturation transfer EPR experiments provide definitive evidence that lipids at the protein interface are exchanging on this timescale. The sensitivity of non-linear EPR to low frequencies of spin exchange also allows the location of spin-labelled membrane protein residues relative to those of spin-labelled lipids, in double-labelling experiments.

Tunable Diode Laser Spectroscopy With Wavelength Modulation: Calibration-Free Measurement of Gas Compositions at Elevated Temperatures and Varying Pressure

The validity of two new approaches to tunable diode laser spectroscopy (TDLS) in the near-IR, namely the residual amplitude modulation approach and the phasor decomposition method, is investigated for application in industrial process monitoring where the operating temperatures and pressures are high and subject to significant change. Both techniques allow the recovery of absolute absorption profile line shapes and are completely calibration free, making them very attractive for online deployment in stand alone instrumentation in harsh environments where the calibration factors in conventional TDLS methods are subject to significant cumulative errors and drift. Currently established TDLS techniques, and indeed conventional gas composition analysis techniques, suffer from significant limitations when applied under these conditions, and there is a clear need for the development of a suitable alternative. The primary focus in this work is the analysis of water vapor in solid oxide fuel cell diagnostics where the operating temperatures range from 700degC to 950degC, the gas pressures are subject to change and the recovered signal levels are low. The 1391.7 nm overtone water vapor transition is interrogated over the above temperature range of interest at concentrations of 6%-50%, while the 1650.96 nm methane transition is also analyzed over a range of gas pressures at a fixed concentration of 1%. Excellent agreement between the experimentally recovered absorption line shapes and simulations based on parameters from the HITRAN (2004) database is observed; further evidence for the efficacy of the techniques is demonstrated through the accuracy of the gas concentration measurements which were achieved by curve-fitting absorption line shape simulations to the experimental data.

Optimized multiple quantum MAS lineshape simulations in solid state NMR

The majority of nuclei available for study in solid state Nuclear Magnetic Resonance have half-integer spin I > 1 / 2 , with corresponding electric quadrupole moment. As such, they may couple with a surrounding electric field gradient. This effect introduces anisotropic line broadening to spectra, arising from distinct chemical species within polycrystalline solids. In Multiple Quantum Magic Angle Spinning (MQMAS) experiments, a second frequency dimension is created, devoid of quadrupolar anisotropy. As a result, the center of gravity of peaks in the high resolution dimension is a function of isotropic second order quadrupole and chemical shift alone. However, for complex materials, these parameters take on a stochastic nature due in turn to structural and chemical disorder. Lineshapes may still overlap in the isotropic dimension, complicating the task of assignment and interpretation. A distributed computational approach is presented here which permits simulation of the two-dimensional MQMAS spectrum, generated by random variates from model distributions of isotropic chemical and quadrupole shifts. Owing to the non-convex nature of the residual sum of squares (RSS) function between experimental and simulated spectra, simulated annealing is used to optimize the simulation parameters. In this manner, local chemical environments for disordered materials may be characterized, and via a re-sampling approach, error estimates for parameters produced. Program summary Program title: mqmasOPT Catalogue identifier: AEEC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3650 No. of bytes in distributed program, including test data, etc.: 73 853 Distribution format: tar.gz Programming language: C, OCTAVE Computer: UNIX/Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron.

Conformational Flexibility of the GM2 Activator Protein Loop Regions Investigated By Site Directed Spin Labeling EPR Spectroscopy

The GM2 activator protein (GM2AP) is an essential component in the degradation pathway of neuronal gangliosides. GM2AP is a required accessory protein for the hydrolytic conversion of GM2 to GM3 by a water soluble hydrolase. The X-ray structure of GM2AP reveals a β-cup topology with multiple conformations of the protein within the unit cell. Because the crystal structures show different conformations of the putative membrane binding loops, we have utilized site-directed spin labeling to investigate conformational flexibility of these loops for protein in solution and bound with GM2 ligand. As such, a series of single and double CYS mutants (still with original 8 CYS in 4 disulfide bridges) have been generated and spin labeled with MTSL. EPR spectra of spin labeled GM2AP were collected with and without GM2 ligand, and no significant changes in the EPR lineshape were seen. EPR spectra were simulated for spin labels located in the loop regions and reveal multiple component fits, while those in the backside of the β-cup beta strands have single component fits. For certain sites in the mobile loops, spectra were acquired as a function of temperature. From these lineshape simulations, the activation energy for the conformational change has been determined. The SDSL EPR results indicate that the multiple conformations observed in the crystallographic unit cell are populated in solution and represent conformational flexibility of the protein; which is not necessarily altered by binding to lipid ligands. Additionally, spin labeled protein was analyzed by mass spectrometry to confirm proper formation of the four disulfide linkages and addition of only one spin label at the mutant cysteine.

A parameterization of the Lyman α and Lyman β line shapes for radiation transport simulations in divertor plasmas

At high divertor densities as foreseen in ITER, the hydrogen resonance radiation is trapped. This significantly affects the divertor dynamics. The model currently used for photon emission and absorption rates in EIRENE has been improved for the Lyman α and Lyman β lines. All line broadening mechanisms in the atom’s rest frame are retained, including Stark, Zeeman and fine structure effects. The influence of the ion dynamics on Stark broadening is described by a computer simulation technique. A parameterization of simulated spectral line shapes is proposed by using a fit subroutine, which allows for fast evaluation of the model in EIRENE.

Effects of jump dynamics on solid state nuclear magnetic resonance line shapes and spin relaxation times

This paper describes EXPRESS ( EXchange Program for RElaxing Spin Systems), a computer program that simulates the effects of Markovian jump dynamics for a wide variety of solid state nuclear magnetic resonance experiments. A graphical interface is described that facilitates the definition of rotational jumps around non-commuting axes that may occur at arbitrary, different rates. Solid state deuteron NMR is widely used to investigate such processes, and EXPRESS allows simulations of deuteron quadrupole echo and magic angle spinning line (MAS) shapes, as well as partially relaxed line shapes for measurements of anisotropic relaxation of Zeeman and quadrupolar order. Facilities are included for chemical shift tensors (at user-defined orientations relative to the quadrupole coupling tensors), so that EXPRESS is potentially useful for studies of paramagnetic systems where these interactions are of comparable magnitude. Many of the same techniques used for deuterons can be extended to half-integer quadrupolar nuclei. The same interface that specifies rotational “sites” for deuteron NMR studies is usable in EXPRESS to simulate static line shapes, MAS line shapes, and multiple pulse Carr–Purcell–Meiboom–Gill (CPMG) line shapes for the central transition of high spin quadrupoles with second order quadrupole coupling and chemical shift anisotropy. Representative simulations are displayed that show effects of slow libration on deuteron quadrupole echo line shapes and relaxation time anisotropies. EXPRESS is also used to investigate fundamental differences in the mechanism of echo formation in deuteron MAS and quadrupole CPMG experiments, and to illustrate significant differences between these techniques in the context of high spin quadrupolar nuclei. The program is modular and platform-independent, with facilities for users to add routines for experiments not yet envisioned.

Molecular dynamics simulation of 13C NMR powder lineshapes of CO in structure I clathrate hydrate

Guest molecules in nonspherical cages of inclusion compounds can possess non-uniform spatial distributions and motion. This can lead to anisotropic lineshapes in the solid-state NMR spectra of the guest species. In this work, we use our previously developed molecular dynamics-based methodology to calculate the lineshape anisotropy of guest CO species in cages of the structure I (sI) clathrate hydrate as an example of the above phenomenon. The linear CO molecules in the oblate large sI clathrate hydrate cages have a preferential alignment in the plane parallel to the two hexagonal faces of the cages. Molecular dynamics simulations are performed at three temperatures in the stability range of the CO sI clathrate to determine the angular distribution of the CO guests in the large and small cages. The experimental (13)C NMR powder lineshapes of CO guests in the large cages become narrower as the temperature is increased from 77 K to 220 K (the limit of the stability of the clathrate). Good agreements between the calculated and experimental powder lineshapes are obtained. No assumptions regarding the nature of the guest motions in the cages are required. The dynamics of guest rotation are characterized by studying the orientational autocorrelation function (OACF) for the CO molecules in the large and small cages at different temperatures.

QuadFit—A new cross-platform computer program for simulation of NMR line shapes from solids with distributions of interaction parameters

A new Java computer program called QuadFit has been written to simulate NMR line shapes from solid materials. The program takes into account the major interactions, with a key feature that distributions of isotropic chemical shift and quadrupolar interaction parameters can be calculated, which are often encountered in amorphous and disordered materials. The quadrupolar interaction can be simulated for all the transitions for both half-integer and integer spins. The utility of the program is demonstrated with examples of 27Al (nuclear spin I = 5 2 ) in an atomically disordered aluminoborate mullite, 65Cu ( I = 3 2 ) in CuInSe 2 and 10B ( I=3) in amorphous B 2O 3. The program has good cross-platform compatibility and is written for high stability. The program has been designed with an easy to use graphical interface. It can be run efficiently on any reasonably powerful PC and is freely available from the Warwick website (http://go.warwick.ac.uk/quadfit).