Pseudopotential-fragment spectroscopy for organic molecules and carbon allotropes

Following on from a previous work (Punter et al., IJQC 2019, 119, 23), pseudopotential sets are developed and tested for a variety of sp² and sp³ carbon fragments. These fragments contain only one or two explicit protons and electrons, and make use of non-atom-centered potentials. They are tested with density functional theory calculations in a selection of chemical environments in which several physical characteristics, including orbital and first ionization energies, are found to be well reproduced. They are then employed in the reproduction of molecular absorption spectra for large organic molecules and carbon allotropes, and are found to recreate both absorption and electronic circular dichroism spectra to a high accuracy. They are also found significantly to increase the computational efficiency of time dependent density functional theory (TDDFT) calculations in which they are used.     

Resonant emission of UO<Subscript>2</Subscript>, U<Subscript>3</Subscript>O<Subscript>8</Subscript>, and UO<Subscript>2+<Emphasis Type="Italic">x</Emphasis></Subscript> valence electrons under SR excitation near the O<Subscript>4,5</Subscript>(U) absorption edge

The structure of the resonant electron emission (REE) spectra of UO₂ (REE appears under the excitation with synchrotron radiation near the O_4,5(U) absorption edge at ∼100 eV and ∼110 eV) is studied with regard to the X-ray O_4,5(U) absorption spectrum of UO₂ and a quantitative scheme of molecular orbitals based on the X-ray electron spectroscopy data and the results of a relativistic calculation of the electronic structure of UO₂. The structure of the REE spectra of U₃O₈ and UO_2+x is studied for comparison, and the effect of the uranium chemical environment in oxides on it is found. The appearance of such a structure reflects the processes of excitation and decay involving the U5d and electrons of the outer valence MOs (OVMOs, from 0 to ∼13 eV) and inner valence MOs (IVMOs, from ∼13 eV to ∼35 eV) of the studied oxides. It is noted that REE spectra show the partial density of states of U6p and U5f electrons. Based on the structure of REE spectra, it is revealed that U5f electrons directly participate (without losing the f nature) in the chemical bonding of uranium oxides and are delocalized within CMOs (in the middle of the band), which results in the enhancement of the intensity of the REE spectra of CMO electrons during resonances. The U6d electrons are found to be localized near the bottom of the outer valence band and are observed in the REE spectra of the studied oxides as a characteristic maximum at 10.8 eV. It is confirmed that U6p electrons are effectively involved in the formation of IVMOs, which leads to the appearance of the structure in the region of IVMO electron energies during resonances. This structure depends on the chemical environment of uranium in the considered oxides.     

High-Resolution Solid-State 13C-NMR Spectroscopy of Polymers [New Analytical Methods (37)]

Until a few years ago, solid-state nuclear resonance yielded spectra containing broad lines only. Meanwhile, CP/MAS-NMR spectroscopy has provided a method which gives narrow nuclear resonance lines from a solid-state specimen as well. Using this technique, it is now possible to produce spectra of “rare” nuclei (¹³C, ²⁹Si, ¹⁵N etc.) which are resolved in terms of chemical structure. The analytical capabilities of NMR spectroscopy can be applied to the solid state: it may be that it is necessary to identify compounds in the solid state because, for example, a solvent would alter the coordination sphere, or that it is desired to monitor chemical reactions in the solid state, for example the baking of an enamel. Where a substance in the solid state is concerned, high-resolution ¹³C-NMR spectroscopy provides not only information about the chemical structure, but also about the solid state itself. To mention just a few examples, information on the conformation, crystal structure and molecular dynamics, as well as molecular miscibility is given. This opens up a broad spectrum of applications, from a statement concerning the crystal modification of an active substance in ready-to-use pharmaceutical preparations, e.g. tablets, to the question of whether two polymers are miscible with one another at a molecular level.     

The Effects of Substituents and Solvents on the Ground‐State π‐Electronic Structure and Electronic Absorption Spectra of a Series of Model Merocyanine Dyes and Their Theoretical Interpretation

Two series of new merocyanine dyes have been synthesised and the dependence of their electronic structure on substituents and solvents has been studied by NMR spectroscopy, by using both the NMR ¹³C chemical shifts between adjacent C atoms in the polymethine chain and the ³J(H,H) coupling constants for trans‐vicinal protons. The widely used valence bond (VB) model based on two contributing structures cannot account theoretically for the observed alternating π‐electron density in the polymethine chain. In addition, the prediction of zero‐π‐bond order alternation (or zero‐bond length alternation) by this model is also incorrect. However, the results are consistent with the predictions of a qualitative VB model which considers the resonance of a positive charge throughout the whole polymethine chain. Based on this model and the Franck‐Condon principle the effect of substituents and solvents on the fine structure of the electronic spectra of these dyes can be explained as vibronic transitions from the vibrational state v=0 to v′, where v is the vibrational quantum number of the totally symmetric C?C valence vibration of the polymethine chain in the electronic ground state and v′ is that in the electronic excited state. In contrast, neither the effects of substituents or solvents on the electronic structure of merocyanines and their electronic spectra can be accounted for by the simple two state VB model.     

The Scent of Maibowle – π Electron Localization in Coumarin from Its Microwave-Determined Structure

The microwave spectra of the natural substance coumarin, a planar aromatic molecule with the specific scent of maibowle, a popular fruit punch served in spring and early summer, were recorded using a molecular jet Fourier transform microwave spectrometer working in the frequency range from 4.0 to 26.5 GHz. The rotational constants and centrifugal distortion constants were determined with high precision, reproducing the spectra to experimental accuracy. The spectra of all singly-substituted ¹³C and ¹⁸O isotopologues were observed in their natural abundances to determine the experimental heavy atom substitution r_s and semi-experimental equilibrium r_e^SE structures. The experimental bond lengths and bond angles were compared to those obtained from quantum chemical calculations and those of related molecules reported in the literature with benzene as the prototype. The alternation of the C−C bond lengths to the value of 1.39 Å found for benzene reflects the localization of π electrons in coumarin, where the benzene ring and the lactone-like chain −CH=CH−(C=O)−O− are fused. The large, negative inertial defect of coumarin is consistent with out-of-plane vibrations of the fused rings.     

Theoretical insight into the magnetic circular dichroism of uranium N6,7-edge X-ray absorption

We use ligand-field density functional theory to determine the electronic structure and to model magnetic circular dichroism in the X-ray absorption spectroscopy (XAS) of uranium compounds. This study extends earlier work on tetravalent uranium ion, in which a model Hamiltonian was set up in order to study electronic structure with three nonequivalent 4f, 5f, and 6d electrons. In the earlier work, the model Hamiltonian took into consideration the interelectron repulsion, spin-orbit coupling interaction, and ligand-field splitting. Uranium N_6,7-edge XAS spectra were calculated on the basis of the 5f² → 4f¹³5f²6d¹ electron transition, showing spectral profiles that were mainly dominated by 4f electron spin-orbit coupling, as well as 6d ligand-field splitting. Fine structures were also observed due to the interelectronic repulsion between 4f-5f, 4f-6d, and 5f-6d electrons. Here, the theoretical study is extended to take into consideration the presence of an external magnetic field, incorporating into the model Hamiltonian for three-open-shell electron configuration a term for Zeeman interaction. Therefore, we are able to model spectra with a left-circularly and right-circularly polarized X-ray, demonstrating evidence of X-ray magnetic circular dichroism (XMCD) for a tetravalent U⁴⁺ ion in the molecular (U(η⁸-C₈H₈)₂) complex. The XMCD originates from a ground-state electronic structure with open-shell 5f electrons. Furthermore, the present calculation of uranium N_6,7-edge XAS and XMCD spectra also enables the ligand-field bonding analysis of the coordination compound.     

Quantitative surface analysis by X-ray photoelectron spectroscopy and X-ray excited auger electron spectroscopy

It is shown that X-ray excited KLL Auger electron spectra allow it to describe measured signal strengths similarly to X-ray photoelectron signals, thus offering valuable information on the quantitative surface composition of a solid sample. The principal equation and corresponding fundamental parameters are discussed. As a result Auger spectra of C, N, O, F, and Na can be easily used in a multiline approach for quantitative analysis. LMM and MNN spectra give rise to more problems, due to their more complicated structure, uncertainties with regard to the background and the influence of Coster-Kronig transitions. These problems are overcome by the use of empirical ratios of the strongest lines of 2p/LMM or 3d/MNN. Since these ratios are independent of sample composition, they allow it to transform the Auger signal into the corresponding photoelectron signal, provided that a standard sample has been measured. Thus a true additional information is obtained and moreover difficulties in cases of photoelectron spectra with overlapping lines from other chemical elements can be overcome.Dedicated to Professor Günther Tölg on the occasion of his 60th birthday     

NMR Spectroscopy of Paramagnetic Complexes

Serviceable NMR spectra can, with a few exceptions^[1,6], be recorded for paramagnetic complexes in solution. These spectra provide information about the structure of the complexes and the distribution of the unpaired electrons, and hence also about reactive centers in the molecule. The elucidation of intermolecular and intramolecular exchange phenomena, e.g. the determination of ligand exchange rate constants, the determination of rotation barriers, and the detection of contact complexes in solution, or even of occupation equilibria of the electrons, is possible in this way. It can be seen, therefore, that NMR studies on paramagnetic complexes can be a rich source of information.     

Computer-assisted structure elucidation of organic compounds III: Automatic fragment generation from13C-NMR spectra

The interpretation of carbon-NMR spectra is mainly based on the comparison with suitable reference data taken from literature. The whole information contents of¹³C-NMR spectra cannot be utilized by manual interpretation. Therefore a network of interactive computer programs has been developed, which simulates the strategy of the spectroscopist in generating structural fragments from the spectral data. The most important knowledge source for this process is a carbon-NMR data base containing some 17,500 spectra. Structural fragments are generated automatically from this data file and assembled by a model builder to complete chemical structures using constraints derived from the spectral data. A comparison of the experimental carbon-NMR spectrum with the estimated ones allows the generation of a sorted hitlist.For part II see: H. Kalchhauser, W. Robien,J. Chem. Inf. Comput. Sci. 1985,25, 103.     

Photoelectron Spectroscopy at the Graphene–Liquid Interface Reveals the Electronic Structure of an Electrodeposited Cobalt/Graphene Electrocatalyst

Electrochemically grown cobalt on graphene exhibits exceptional performance as a catalyst for the oxygen evolution reaction (OER) and provides the possibility of controlling the morphology and the chemical properties during deposition. However, the detailed atomic structure of this hybrid material is not well understood. To elucidate the Co/graphene electronic structure, we have developed a flow cell closed by a graphene membrane that provides electronic and chemical information on the active surfaces under atmospheric pressure and in the presence of liquids by means of X‐ray photoelectron spectroscopy (XPS). We found that cobalt is anchored on graphene via carbonyl‐like species, namely Co(CO)_x, promoting the reduction of Co³⁺ to Co²⁺, which is believed to be the active site of the catalyst.     

Mechanical relaxation spectroscopy of three triepoxide-based polymers

Three network structure polymers formed by the chemical reactions of a triepoxide with aniline, 3-chloroaniline,and 4-chloroaniline were prepared and their shear modulus relaxation spectra studied over the 10⁻³- to 1-Hz range and temperatures up to their rubber modulus region. The decrease in the unrelaxed modulus with increase in temperature is found to be a reflection of both an increase in volume, and a decrease in the relaxed modulus of the sub-T_g relaxations process. It is quantitatively shown that the increase in the rubber modulus with increase in temperature above T_g is predominantly due to an increase in the entropy and not to a decrease in the number of cross-links density on thermal expansion. The unrelaxed modulus remained unaffected by the change in the overall size of the phenyl groups of the amines and of the steric hindrance to their rotations caused by the proximity of the chlorine atom to the cross-linking N-atom in the network structure, but the rubber modulus was effected. The shear modulus spectra could be fitted to a stretched exponential decay function with a temperature-independent stretch parameter of 0.25 for two polymers and 0.22 for one. The time–temperature superposition of the spectra did not yield a master curve, and a vertical displacement of the data also failed to produce it. This was more clearly demonstrated by the spectra of the mechanical loss tangent. After considering the various contributions to the shear modulus, it was concluded that deviations from the time–temperature superposition of the spectra are intrinsic to these polymers and arise from the change in the viscoelastic functions for segmental dynamics on change in the temperature such that the overall distribution of relaxation times remains unaffected. The mechanical loss tangent of the three polymers is found to be higher than that of polycarbonate at ambient temperature, implying a higher loss of mechanical energy before these polymers may fracture. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 3071–3083, 1999     

Preparation and Characterization of Pure Thiosulfuric Acid

Pure thiosulfuric acid has not been prepared yet, although it is described in most textbooks of inorganic chemistry. Furthermore, no experimental evidence for the structure of thiosulfuric acid is known. Theoretical calculations predict the (SH)(OH) tautomer to be more stable than the (OH)(OH) tautomer. In this work we present the synthesis and spectroscopical characterization of pure thiosulfuric acid. X₂S₂O₃ (X = H, D) was obtained from the reaction of dry Na₂S₂O₃ with anhydrous HF at –60 °C. The experimental vibrational and NMR spectra together with quantum chemical calculations provide evidence for the predicted (SH)(OH) tautomeric structure.     

Extended NMR Study of Spin-Crossover Compounds [Fe(1-alkyl-1H-tetrazole)6](BF4)2 and Their ZnII Analogs

A systematic NMR study was performed on several alkyl–tetrazole complexes of iron(II) and zinc(II) in the 10–300 K temperature range. The experiments were designed to separate the electronic and reorientational phase transitions caused by the spin crossover of the iron compounds from those independent of unpaired electrons. The ¹⁹F spectral data on the propyl-tetrazole compounds show that the electronic spin-transition has a strong effect on the spectra, and their behavior can be explained as a combined response to molecular reorientations and the spin transition. For these complexes, second-moment calculations revealed the strength of the interaction between resonant and nonresonant nuclei. Both of the applied NMR methods show irregularities at the temperature region between 70 and 120 K, suggesting the presence of a phase transition. The data also suggest two kinds of reorientational behavior for the BF₄ ^– counter ions. In the iron–ethyl–tetrazole compound, unlike in the propyl–tetrazole complex, a significant amount of unpaired electrons remains in their original high-temperature HS state. Above their effect, the behavior of the nuclear spins of the iron compound is basically governed by the same structural factors as in its zinc analog. The two-exponential behavior of the ¹H-T ₁ in case of the zinc–methyl–tetrazole compound can be explained on the basis of cross relaxation with the ¹⁹F nuclei due to the low ¹H/¹⁹F ratio. The presence of the two types of methyl reorientation is assumed to be the sign of the two different lattice sites known to be present in the Fe^II compound. The single-exponential T ₁ above T _c in the case of [Fe(mtz)₆](BF₄)₂ is consistently the sign of the strength of the paramagnetic relaxation observed in the ethyl and propyl compounds.     

Environmental Effects in Computational Spectroscopy: Accuracy and Interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical–chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.     

Structural and dynamical aspects of PEG/LiClO4 in solvent mixtures via NMR spectroscopy

Motivated by the potential usefulness of polyethylene glycol (PEG)/Li⁺ salt mixtures in several industrial applications, we investigated the structure and dynamics of PEG/LiClO₄ mixtures in D₂O and its mixtures with CD₃CN and DMSO-d₆, in a series of PEG-based polymers with a wide variation in their molecular weights. ¹H NMR chemical shifts, T₁/T₂ relaxation rates, pulsed-field gradient NMR diffusion experiments, and 2D HOESY NMR studies have been performed to understand the structural and dynamical aspects of these mixtures. Increasing the temperature of the medium results in a significant perturbation in the H-bonded structure of PEG in its PEG/LiClO₄/D₂O mixtures as observed from the increase in chemical shifts. On the other hand, the addition of molecular cosolvents has a negligible effect. The hydrodynamic structure of PEG shows a pronounced variation at low temperature with increasing molecular weight, which, however, disappears at higher temperatures. Increasing the temperature leads to a decrease in the hydrodynamic structure of PEG, which can be explained on the basis of solvation–desolvation phenomena. The 2D HOESY NMR spectra reveal a new finding of Li⁺-water binding in the PEG/LiClO₄/D₂O mixtures with the addition of molecular solvents, suggesting that the Li⁺ cation diffuses freely in the D₂O mixtures of polymers as compared with the polymer mixtures with DMSO or CD₃CN.     

Far infrared fourier transform spectroscopy of semiconductors

Fourier transform spectroscopy (FTS) is one of the most important tools in the study of shallow level donors and acceptors in semiconductors. When combined with a two-step photothermal ionization process detected photoconductively, FTS allows measurement of optical transitions of donor-bound electrons (and acceptor-bound holes) in ultra-pure germanium samples with impurity concentrations <10⁹ cm^–3 (i.e. one electrically active impurity in 4×10¹³ host atoms). The experimental high resolution study of the hydrogen-like excited state series of shallow levels has yielded as many as 19 lines of width as small as 10eV for some centers. These results have stimulated theoretical work which has led to the unambiguous assignment of quantum states to many bound excited states. Extensive studies of ultra-pure Ge crystals grown under different well-controlled conditions have led to the discovery of a large number of novel shallow impurity complexes. Study of the multiplicities and symmetries of the associated electronic states has led to a detailed understanding of the unusual static and dynamic structures of these novel centers. The chemical composition has been deduced from correlations between the concentration of a particular center and the materials involved in crystal gowth. Isotopic substitution of hydrogen with deuterium has led to the unambiguous proof of the presence of hydrogen in several of the novel centers. In addition to the high resolution spectra of shallow electronic levels, vibrational spectra of bond-centered interstitial oxygen in ultra-pure Ge are noteworthy for their extraordinarily sharp lines.     

An Investigation of Lanthanum Coordination Compounds by Using Solid‐State 139La NMR Spectroscopy and Relativistic Density Functional Theory

Lanthanum‐139 NMR spectra of stationary samples of several solid La^III coordination compounds have been obtained at applied magnetic fields of 11.75 and 17.60 T. The breadth and shape of the ¹³⁹La NMR spectra of the central transition are dominated by the interaction between the ¹³⁹La nuclear quadrupole moment and the electric field gradient (EFG) at that nucleus; however, the influence of chemical‐shift anisotropy on the NMR spectra is non‐negligible for the majority of the compounds investigated. Analysis of the experimental NMR spectra reveals that the ¹³⁹La quadrupolar coupling constants (C_Q) range from 10.0 to 35.6 MHz, the spans of the chemical‐shift tensor (Ω) range from 50 to 260 ppm, and the isotropic chemical shifts (δ_iso) range from ?80 to 178 ppm. In general, there is a correlation between the magnitudes of C_Q and Ω, and δ_iso is shown to depend on the La coordination number. Magnetic‐shielding tensors, calculated by using relativistic zeroth‐order regular approximation density functional theory (ZORA‐DFT) and incorporating scalar only or scalar plus spin–orbit relativistic effects, qualitatively reproduce the experimental chemical‐shift tensors. In general, the inclusion of spin–orbit coupling yields results that are in better agreement with those from the experiment. The magnetic‐shielding calculations and experimentally determined Euler angles can be used to predict the orientation of the chemical‐shift and EFG tensors in the molecular frame. This study demonstrates that solid‐state ¹³⁹La NMR spectroscopy is a useful characterization method and can provide insight into the molecular structure of lanthanum coordination compounds.     

Magnetic Resonance of Paramagnetic Complexes

The line width of the ESR and NMR signals of paramagnetic transition metal complexes is determined mainly by the electron spin-lattice relaxation time τ_e. Values of τ_e greater than 10^?9 lead to ESR spectra that are readily resolved, while values smaller than 10^?11 give NMR spectra having small line widths. Since fast relaxation processes are effective in nearly all transition metal complexes with several unpaired electrons and in all complexes having an orbitally degenerate ground state, the NMR method has a wider scope. The sign and magnitude of the electron-nucleus coupling can be determined with great sensitivity from the NMR spectra, whereas only the magnitude of this interaction can be determined from the ESR spectra. Free spin densities can be found very accurately from the NMR shifts, and the method can therefore be advantageously applied to kinetic measurements, e.g. on short-lived contact complexes.