Lineshape Simulations Research Articles

First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate

Using a first-principles approach, we calculate electronic and optical properties of molecular aggregates of the dye amphi-pseudoisocyanine, whose structures we obtained from molecular dynamics (MD) simulations of the self-aggregation process. Using quantum chemistry methods, we translate the structural information into an effective time-dependent Frenkel exciton Hamiltonian for the dominant optical transitions in the aggregate. This Hamiltonian is used to calculate the absorption spectrum. Detailed analysis of the dynamic fluctuations in the molecular transition energies and intermolecular excitation transfer interactions in this Hamiltonian allows us to elucidate the origin of the relevant time scales; short time scales, on the order of up to a few hundreds of femtoseconds, result from internal motions of the dye molecules, while the longer (a few picosecond) time scales we ascribe to environmental motions. The absorption spectra of the aggregate structures obtained from MD feature a blue-shifted peak compared to that of the monomer; thus, our aggregates can be classified as H-aggregates, although considerable oscillator strength is carried by states along the entire exciton band. Comparison to the experimental absorption spectrum of amphi-PIC aggregates shows that the simulated line shape is too wide, pointing to too much disorder in the internal structure of the simulated aggregates.

Computational Investigation on the Spectroscopic Properties of Thiophene Based Europium β-Diketonate Complexes.

The adiabatic transition energies from the lowest triplet states of four Europium tris β-diketonate/phenantroline complexes have been determined in vacuo and in dicholomethane solution by the ΔSCF approach at the density functional theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals. The calculated adiabatic transition energies have been compared with the experimental 0-0 transitions of each complex determined from phosphorescence spectra of the corresponding Gd(3+) complexes and followed by direct comparison between simulated and experimental spectra line shapes. For compound 1, the Eu(TTA)3Phen system, triplet states other than the lowest one and conformational isomers other than the one present in the crystallographic structure have been considered. In the crystallographic structure, this compound presents three quasi-degenerate low energy triplet states, differing for the TTA ligand where the two unpaired electrons are localized and showing close adiabatic transition energies. For compound 1, the lowest triplet states of the four investigated conformational isomers show similar characteristics and close adiabatic transition energies. On the basis of these results, an investigation of compounds 2-4 (Eu(Br-TTA)3Phen, Eu(DTDK)3Phen, and Eu(MeT-TTA)3) has been performed by considering only the isomer present in the crystallographic structure and only the lowest triplet state of each compound. For compounds 1-3, the energies of the lowest triplet states calculated by both functionals in solution including zero-point energy corrections well reproduce the experimental trends as well as the values of the adiabatic transition energies: CAM-B3LYP, the best performing functional, provides energies of the lowest triplet state with deviations from experiments lower than 1200 cm(-1). Also, the calculated vibrationally resolved phosphorescence spectra and UV-vis absorptions well reproduce the main features of their experimental counterparts. Significant differences between calculated and experimental results are observed for compound 4, for which difficulties in the experimental determination of the triplet state energy were encountered: our results show that the negligible photoluminescence quantum yield of this compound is due to the fact that the energy of the most stable triplet state is significantly lower than that of the resonance level of the Europium ion, and thus the energy transfer process is prevented. These results confirm the reliability of the adopted computational approach in calculating the energy of the lowest triplet state energy of these systems, a key parameter in the design of new ligands for lanthanide complexes presenting large photoluminescence quantum yields.

Theoretical and experimental determination of the absorption and emission spectra of a prototypical indolenine-based squaraine dye

The spectroscopy of a prototypical indolenine-based squaraine dye is analysed theoretically using state-of-the-art methodologies for the simulation of spectral lineshapes, and experimentally using optical absorption and emission spectroscopies. Density functional theory and its time-dependent extension are used to determine the stability of several conformers, to compute their excitation energies, equilibrium geometries and vibrational frequencies, both in the ground and in their first excited singlet state. Finally the generating function approach is used to simulate the vibronic lineshape of the low energy valence ππ* excitation and emission spectra. Solvent effects are also computed and discussed by using the polarizable continuum model. The developed model correctly reproduces the main spectral features of the squaraine, and allows us to identify the vibrational motions that mainly contribute to the observed lineshape.

A Simulation Study of the Far-Infrared Absorption Spectra of HCl Diluted in Liquid Ar

The far-infrared absorption coefficient of HCl diluted in liquid Ar has been calculated by using a mixed classical-quantum stochastic simulation approach. The simulated spectra have been compared with the available experimental data at different thermodynamic conditions without using ad hoc fitting parameters. Despite the fact that some discrepancies can be observed in the high frequency side of the far-infrared bands, a reasonable agreement has been found between the theoretical and the experimental spectral profiles. Both, classical and quantum simulated line shapes were comparatively analyzed, determining the time scales involved in the rotational spectra.

Anomalous EPR Intensity Distribution of the Methyl Radical Quartet Adsorbed on the Surface of Porous Materials. Comparison with Solid Gas Matrix Isolation

The two inner lines of the EPR quartet of methyl radicals trapped in cryogenic gas matrices are superpositions of the inner transitions of an A-proton-spin quartet and an E-proton-spin doublet. Their intensity relative to the outer lines provides information on the population of the methyl-rotation quantum states. The above intensity ratio for the CH3 in solids is a challenging problem of the quantum dynamics and statistical thermodynamics. The influence of the quantum-mechanical/inertial rotation on the intensity distribution of the hf components of methyl radical on the surface of porous materials, e.g., silica gel, is investigated by EPR line shape simulations and compared with spectra of the radical isolated in the bulk of solid gas samples. The experimental part of this study includes the first in literature EPR observation of methyl radical in the bulk of N2O solid and provides new essential information on CH3 in CO2 and Ar matrices, thus, covering both strongly hindered and almost free rotation of the radical. We verify the observation of nonrotating methyl radicals in a N2O matrix, discovered earlier in cold CO2, give a thorough account of their EPR characteristics, and explore their formation at the inner surface of porous materials. Combination of a classical spin-Hamiltonian with employment of quantum effects due to nuclear spin-rotation coupling and the radical symmetry were used to interpret the experimental spectral observations. The cause of experimentally found unexpected contribution of the excited degenerate E-doublets to the EPR spectrum down to 4.2 K and A/E transition amplitude ratios sometimes as high as ca. 1:8 at liquid-N2 temperature is sought. The validity of Bose-Einstein quantum (BEq-) statistics of the spin rotation states in addition to the classical Maxwell-Boltzmann (Boltzmann) statistics was also assessed against experimental population A/E-ratio data. The BEq-statistics were not previously applied to similar systems. Furthermore, detailed consideration of the laboratory/free space rotational degeneracy and the planarity of methyl radical was also included in this work.

Dynamics of Ag+ Ions in RbAg4I5 Probed Indirectly via 87Rb Solid-State NMR

Solid-state 87Rb NMR has been used to determine the ionic hopping rate of Ag+ ions in a powdered sample of α-RbAg4I5 as a function of temperature from 20 to 250 °C. In this phase, Rb is a stationary framework atom, which does not take part in ionic conduction in this material. At the same time 87Rb has a large quadrupole moment, making 87Rb NMR capable of detecting mobile species in close proximity. Simulation of the static 87Rb NMR powder pattern under the influence of Ag+ motion was performed using the EXPRESS software. Lineshape simulations were used to extract an ionic hopping rate for each temperature, and changes in the line shape were correlated to changes in ion mobility, which increases with temperature. Ag+ hopping rates were found to be in the range of 7.0 ± 0.5 kHz to 30 ± 2 kHz within the temperature window of 20 to 100 °C, resulting in an activation energy of 17 ± 3 kJ/mol (0.18 ± 0.03 eV), for silver ion hopping. This result is in agreement with previous studies, suggesting that this indire...

Magnetic defects in crystalline Zn(OH)2 and nanocrystalline ZnO resulting from its thermal decomposition

Trace amounts of substitutional Mn2+ ions and shallow donors magnetic centers were identified by electron paramagnetic resonance (EPR) in crystalline Zn(OH)2 prepared by precipitation of a Zn-nitrate solution with NaOH. Strong changes in the Mn2+ ions spectrum, as well as a sharp increase in the concentration of the shallow donor centers were observed by EPR in the 110–140°C temperature range, during pulse annealing experiments in air up to 240°C. They reflect the decomposition of the crystalline Zn(OH)2 host lattice into nanocrystalline ZnO, confirmed by X-ray diffraction and thermal analysis measurements. Accurate spin Hamiltonian parameters of the observed paramagnetic centers were determined by lineshape simulation and fitting of the EPR spectra, to be used as reference data in further studies of nanocrystalline systems involving Zn(OH)2.

EPR Studies on Branched High‐Spin Arylnitrenes

The UV (λ>305 nm) photolysis of triazide 3 in 2-methyl-tetrahydrofuran glass at 7 K selectively produces triplet mononitrene 4 (g=2.003, D(T)=0.92 cm(-1), E(T)=0 cm(-1)), quintet dinitrene 6 (g=2.003, D(Q)=0.204 cm(-1), E(Q)=0.035 cm(-1)), and septet trinitrene 8 (g=2.003, D(S)=-0.0904 cm(-1), E(S) =-0.0102 cm(-1)). After 45 min of irradiation, the major products are dinitrene 6 and trinitrene 8 in a ratio of ∼1:2, respectively. These nitrenes are formed as mixtures of rotational isomers each of which has slightly different magnetic parameters D and E. The best agreement between the line-shape spectral simulations and the experimental electron paramagnetic resonance (EPR) spectrum is obtained with the line-broadening parameters Γ(E(Q))=180 MHz for dinitrene 6 and Γ(E(S))=330 MHz for trinitrene 8. According to these line-broadening parameters, the variations of the angles Θ in rotational isomers of 6 and 8 are expected to be about ±1 and ±3°, respectively. Theoretical estimations of the magnetic parameters obtained from PBE/DZ(COSMO)//UB3LYP/6-311+G(d,p) calculations overestimate the E and D values by 1 and 8 %, respectively. Despite the large distances between the nitrene units and the extended π systems, the zero field splitting (zfs) parameters D are found to be close to those in quintet dinitrenes and septet trinitrenes, where the nitrene centers are attached to the same aryl ring. The large D values of branched septet nitrenes are due to strong negative one-center spin-spin interactions in combination with weak positive two-center spin-spin interactions, as predicted by theoretical considerations.

Direct simulation of magnetic resonance relaxation rates and line shapes from molecular trajectories.

We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.

Direct Investigation of Covalently Bound Chlorine in Organic Compounds by Solid‐State 35Cl NMR Spectroscopy and Exact Spectral Line‐Shape Simulations

35/37Cl NMR spectroscopy studies of organic systems are very rare, with only a few neat liquids having been studied.1 The lack of chlorine NMR spectroscopy data may be explained by the fact that 35Cl and 37Cl are quadrupolar (spin I=3/2) and low-frequency isotopes. The quadrupole moments of the chlorine nuclei couple with the electric field gradient (EFG) tensor at the nuclei; this phenomenon is known as the quadrupolar interaction (QI). The quadrupolar coupling constant, CQ, and the quadrupolar asymmetry parameter, ηQ, describe the magnitude and asymmetry of the QI. In solution, one of the consequences of the QI is fast relaxation, which means that the 35/37Cl NMR signals for covalently bound chlorines are very broad and are of low intensity.1 For these reasons, chemically distinct chlorine sites are very difficult to distinguish with solution NMR spectroscopy. However, in the solid state, nuclear spin relaxation is typically slower, thus enabling higher quality 35Cl NMR spectra to be collected, at least in principle. Unfortunately, the magnitude of the QI for covalently bound chlorines is very large because of the substantial, anisotropic EFG at the Cl atom, owing mainly to its electronic configuration when it forms a chlorine–carbon bond. Conventional wisdom is that such chlorine sites cannot be studied in powders by solid-state NMR spectroscopy as the central transition (CT; mI=1/2↔−1/2) can span tens of megahertz in typical commercially available magnetic fields. For this reason, only ionic chlorides2 and inorganic chlorides3 have been studied, as the EFG at these chlorides is often an order of magnitude smaller than at covalently bound chlorine atoms in organic molecules. The bonding environments for these types of chlorine atoms are substantially different from the environments in those chloride-containing molecules that have been studied previously.2, 3 A partial 35Cl NMR spectrum for hexachlorophene has been briefly mentioned in the literature.4 On the other hand, most of the interesting chlorine chemistry occurs when Cl is covalently bound to a carbon atom, where the chlorine atom often acts as a leaving group. Chlorine atoms are also important in many organic pharmaceuticals as well as in crystal design applications where they can form halogen bonds.5 Recent studies show that covalently bound chlorine is also important in biological chemistry where, for example, the tryptophan 7-halogenase was found to selectively chlorinate tryptophan moieties.6

Quantitative Analysis of Multisite Protein–Ligand Interactions by NMR: Binding of Intrinsically Disordered p53 Transactivation Subdomains with the TAZ2 Domain of CBP

Determination of affinities and binding sites involved in protein-ligand interactions is essential for understanding molecular mechanisms in biological systems. Here we combine singular value decomposition and global analysis of NMR chemical shift perturbations caused by protein-protein interactions to determine the number and location of binding sites on the protein surface and to measure the binding affinities. Using this method we show that the isolated AD1 and AD2 binding motifs, derived from the intrinsically disordered N-terminal transactivation domain of the tumor suppressor p53, both interact with the TAZ2 domain of the transcriptional coactivator CBP at two binding sites. Simulations of titration curves and line shapes show that a primary dissociation constant as small as 1-10 nM can be accurately estimated by NMR titration methods, provided that the primary and secondary binding processes are coupled. Unexpectedly, the site of binding of AD2 on the hydrophobic surface of TAZ2 overlaps with the binding site for AD1, but AD2 binds TAZ2 more tightly. The results highlight the complexity of interactions between intrinsically disordered proteins and their targets. Furthermore, the association rate of AD2 to TAZ2 is estimated to be 1.7 × 10(10) M(-1) s(-1), approaching the diffusion-controlled limit and indicating that intrinsic disorder plus complementary electrostatics can significantly accelerate protein binding interactions.

An EPR Study on Nanographites

We present the results of an electron paramagnetic resonance study (EPR) in the range of 4–290 K on samples of nanographites obtained by ball milling graphite for different times. With a careful simulation of the spectral line shapes, we disentangled the EPR bands, providing the spectral profiles and intensities of the components on varying the temperature, their g tensors, and the homogeneous line widths of the contributing spin packets. We have been able to follow the effect of decreasing progressively the size of the flakes on the EPR bands due to mobile electrons and on Lorentzian lines due to nonbonding electrons on the zigzag edges of the crystallites. The temperature dependence of the EPR intensities shows a common trend for the signals attributed to edge electrons and to mobile electrons, showing that they belong to the same bath.

Water molecular reorientation in ice and tetrahydrofuran clathrate hydrate from lineshape analysis of 17O spin-echo NMR spectra

Lineshape analysis of 17O spin-echo NMR spectra has been used to study water molecular reorientations in ice-Ih and THF Structure II clathrate hydrate. The kinetics was determined by the changes of the lineshapes of the 17O central transitions at different temperatures. A model involving 12 orientations and 4-step jumps of water molecular orientations was proposed. Semi-classical exchange formalism was employed to simulate the lineshape of the central transitions of the 17O nuclei. Lineshape analysis gave the quadrupolar coupling constant CQ = 6.43 MHz and the asymmetry parameter η = 0.935, for both ice-Ih and THF gas hydrate. The theoretical lineshape simulations resulted in activation energies of water molecular reorientations Ea = 55.2 ± 2.1 kJ mol–1 and Ea = 30.5 ± 0.8 kJ mol–1 for ice-Ih and THF hydrate, respectively. The range of dynamic rates in THF clathrate hydrate is such that before melting, a pseudo-isotropic lineshape is observed that retains a second-order quadrupolar shift. The water reorientation process is discussed in light of recent results on Bjerrum defect injection obtained from molecular dynamics simulation and structural studies.

Mixed-Valence State of a Pyrazine-Bridged Dimer of Oxocarboxylatotriruthenium Complexes with a Nitrosyl Ligand

Three new pyrazine-bridged dimers of oxoacetatotriruthenium with an NO ligand are synthesized. These complexes show two types of stable mixed-valence states. The ν(NO) stretches for five oxidation states were obtained, and the intramolecular electron-transfer rate within the mixed-valence state is evaluated from the IR spectral line-shape simulation based on Bloch-type analysis, which is the first application of this method to a spectator ligand of NO.

Mobility of Solid tert-Butyl Alcohol Studied by Deuterium NMR

The molecular mobility of solid deuterated tert-butyl alcohol (TBA) has been studied over a broad temperature range (103–283 K) by means of solid-state 2H NMR spectroscopy, including both line shape and anisotropy of spin–lattice relaxation analyses. It has been found that, while the hydroxyl group of the TBA molecule is immobile on the 2H NMR time scale (τC > 10(–5) s), its butyl group is highly mobile. The mobility is represented by the rotation of the methyl [CD3] groups about their 3-fold axes (C3 rotational axis) and the rotation of the entire butyl [(CD3)3-C] fragment about its 3-fold axis (C3′ rotational axis). Numerical simulations of spectra line shapes reveal that the methyl groups and the butyl fragment exhibit three-site jump rotations about their symmetry axes C3 and C3′ in the temperature range of 103–133 K, with the activation energies and preexponential factors E1 = 21 ± 2 kJ/mol, k(01) = (2.6 ± 0.5) × 10(12) s(–1) and E2 = 16 ± 2 kJ/mol, k(02) = (1 ± 0.2) × 10(12) s(–1), respectively. Analysis of the anisotropy of spin–lattice relaxation has demonstrated that the reorientation mechanism of the butyl fragment changes to a free diffusion rotational mechanism above 173 K, while the rotational mechanism of the methyl groups remains the same. The values of the activation barriers for both rotations at T > 173 K have the values, which are similar to those at 103–133 K. This indicates that the interaction potential defining these motions remains unchanged. The obtained data demonstrate that the detailed analysis of both line shape and anisotropy of spin–lattice relaxation represents a powerful tool to follow the evolution of the molecular reorientation mechanisms in organic solids.

Electron Spin Relaxation and Heterogeneity of the 1:1 α,γ-Bisdiphenylene-β-phenylallyl (BDPA)/Benzene Complex

The electron spin-spin relaxation time (T(2)) for the 1:1 crystalline complex of α,γ-bisdiphenylene-β-phenylallyl (BDPA) with benzene was determined by continuous wave (CW) and rapid scan electron paramagnetic resonance (EPR). T(2) for individual BDPA particles found by simulation of rapid scan spectra or by simulation of the Lorentzian line shapes of CW spectra were in good agreement. The T(2) for small BDPA particles in air ranged from 80 to 160 ns, which corresponds to peak-to-peak Lorentzian linewidths of 0.82-0.41 G. The removal of oxygen from the samples had a greater impact on the line width for particles that had shorter T(2) in air. Heterogeneity in the g-value was not observed at X-band. Scanning electron microscope (SEM) images showed that the BDPA particles had varying morphology.

Q-Band EPR Spectroscopy of Photogenerated Quartet State Organic Nitreno Radicals

Q-band 34 GHz EPR spectra are reported for quartet state 2-(para-nitrenophenyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl and 3-(para-nitrenophenyl)-1,5,6-triphenylverdazyl reactive intermediates generated from the corresponding azido precursors under frozen matrix photochemical conditions, in situ in a Q-band resonator. Comparison of the Q-band spectra to those generated under conventional X-band (9-10 GHz) conditions shows the much superior resolution of transitions in the g > 2 region of the former. Spectral transitions assigned by line shape simulation yield the zero field splittings for the nitreno-radical species.

Accurate determination of the spin Hamiltonian parameters for Mn 2+ ions in cubic ZnS nanocrystals by multifrequency EPR spectra analysis

Accurate determination of the spin Hamiltonian (SH) parameters, describing the electron paramagnetic resonance (EPR) spectra of paramagnetic impurity ions in wide band gap semiconductor nanocrystals, is essential for determining their localization and quantum properties. Here we present a procedure, based on publicly available software, for determining with higher accuracy the SH parameters of isolated Mn 2+ impurity ions in small cubic ZnS nanocrystals. The procedure, which can be applied to other cubic II–VI semiconductor nanocrystals as well, is based on the analysis of both low and high frequency EPR spectra with line shape simulation and fitting computing programs, which include the hyperfine forbidden transitions and line broadening effects. The difficulties, limitations and errors which can affect the accuracy in determining some of the SH parameters are also discussed.

Characterizing Induced-Conformational Changes in Intrinscially Disordered Proteins via Multi-Frequency EPR Spectroscopy

Intrinsically disordered proteins (IDPs) contain little to no secondary or tertiary structure and are often essential in biological systems. Many IDPs undergo a conformational change, where structure is induced upon binding to its target protein. Due to their very nature, structural studies of IDPs are often challenging. Here, we show how a multi-frequency approach to site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy can be utilized to characterize the mobility and conformational changes of IDPs. We have applied this method to IA3, which is a 68 residue IDP whose unstructured-to-α-helical conformational transition has been extensively characterized by various biophysical techniques. We monitored the induced conformational change in the presence of the secondary structural stabilizer 2,2,2-trifluoroethanol (TFE), at both X-, and W-band frequencies. Analyses of the X-band EPR spectral line shapes reveal that the data report on global correlation time changes consistent with a two-state model of an unstructured system and the tumbling of a rigid helix; more detailed analyzes of the X-band spectral line shapes can provide site-specific information on the residue level. Analysis of the W-band EPR spectral line shapes, however, more directly reveal site-specific structural changes. Line shape simulations of the data at both frequencies should provide further information on the site-specific conformational changes occurring in the presence of TFE and are currently underway. Using IA3 as a model system, we show multi-frequency EPR can provide insight into structural changes occurring in IDP systems that are otherwise difficult to characterize.

A master-equation approach to the description of proton-driven spin diffusion from crystal geometry using simulated zero-quantum lineshapes

Measurements of proton-driven carbon-13 spin diffusion (PDSD) by NMR spectroscopy are a central component of structural analyses of biomolecules in the solid-state. However, the quantitative link between experimental PDSD data and structural information is difficult to make. Here we observe that a master-equation approach can be used to model full PDSD dynamics accurately in polycrystalline (13)C-labelled L-histidine·HCl·H(2)O under magic-angle spinning. In the master-equation approach, PDSD rates and effective dipolar couplings are related by a function of the carbon-carbon zero-quantum lineshapes; we find that numerical simulations of the zero-quantum lineshapes are sufficiently accurate so as to allow the calculation of PDSD rates that are in good agreement with the measured rates, directly from crystal geometry and with no adjustable parameters. Finally, using carbon-carbon internuclear distances we illustrate the potential of the master-equation approach for structural studies. Generalisation of these results to proton-driven carbon-13 spin diffusion in more complex molecular systems is readily envisaged.