Nuclear inelastic scattering and Mössbauer spectroscopy as local probes for ligand binding modes and electronic properties in proteins: vibrational behavior of a ferriheme center inside a β-barrel protein

In this work, we present a study of the influence of the protein matrix on its ability to tune the binding of small ligands such as NO, cyanide (CN(-)), and histamine to the ferric heme iron center in the NO-storage and -transport protein Nitrophorin 2 (NP2) from the salivary glands of the blood-sucking insect Rhodnius prolixus. Conventional M?ssbauer spectroscopy shows a diamagnetic ground state of the NP2-NO complex and Type I and II electronic ground states of the NP2-CN(-) and NP2-histamine complex, respectively. The change in the vibrational signature of the protein upon ligand binding has been monitored by Nuclear Inelastic Scattering (NIS), also called Nuclear Resonant Vibrational Spectroscopy (NRVS). The NIS data thus obtained have also been calculated by quantum mechanical (QM) density functional theory (DFT) coupled with molecular mechanics (MM) methods. The calculations presented here show that the heme ruffling in NP2 is a consequence of the interaction with the protein matrix. Structure optimizations of the heme and its ligands with DFT retain the characteristic saddling and ruffling only if the protein matrix is taken into account. Furthermore, simulations of the NIS data by QM/MM calculations suggest that the pH dependence of the binding of NO, but not of CN(-) and histamine, might be a consequence of the protonation state of the heme carboxyls.     

Mesoporous silica nanoparticles in biomedical applications

This tutorial review provides an outlook on nanomaterials that are currently being used for theranostic purposes, with a special focus on mesoporous silica nanoparticle (MSNP) based materials. MSNPs with large surface area and pore volume can serve as efficient carriers for various therapeutic agents. The functionalization of MSNPs with molecular, supramolecular or polymer moieties, provides the material with great versatility while performing drug delivery tasks, which makes the delivery process highly controllable. This emerging area at the interface of chemistry and the life sciences offers a broad palette of opportunities for researchers with interests ranging from sol-gel science, the fabrication of nanomaterials, supramolecular chemistry, controllable drug delivery and targeted theranostics in biology and medicine.     

Broadly wavelength- and pulse width-tunable high-repetition rate light pulses from soliton self-frequency shifting photonic crystal fiber integrated with a frequency doubling crystal

Soliton self-frequency shift (SSFS) in a photonic crystal fiber (PCF) pumped by a long-cavity mode-locked Cr:forsterite laser is integrated with second harmonic generation (SHG) in a nonlinear crystal to generate ultrashort light pulses tunable within the range of wavelengths from 680 to 1800?nm at a repetition rate of 20?MHz. The pulse width of the second harmonic output is tuned from 70 to 600?fs by varying the thickness of the nonlinear crystal, beam-focusing geometry, and the wavelength of the soliton PCF output. Wavelength-tunable pulses generated through a combination of SSFS and SHG are ideally suited for coherent Raman microspectroscopy at high repetition rates, as verified by experiments on synthetic diamond and polystyrene films.     

Assessment of Subgrid-Scale Models for Decaying Compressible MHD Turbulence

Large eddy simulation method is formulated for study of compressible magnetohydrodynamic turbulence and assessment of different subgrid-scale models as applied for decaying case is performed. The filtered equations of compressible magnetopause using the mass-weighted filtering operation are obtained. Mass-weighted filtered equations for large-scale turbulent component comprise subgrid-scale terms and five models for closure of the subgrid-scale terms are suggested. In present paper the obtained results of numerical computations for large eddy simulation are compared with the results of direct numerical simulation of three-dimensional compressible magnetohydrodynamic turbulence. Assessment of five subgrid-scale models of large eddy simulation for MHD flows is fulfilled. The comparisons between large eddy simulation and direct numerical simulation are carried out regarding the temporal evolution of the global quantities kinetic and magnetic energy, cross helicity and the spectra of kinetic and magnetic energy.     

Phosphorylation of imidazo[2,1‐b]thiazoles with phosphorus(III) halides in the presence of bases

The reaction of phosphorus(III) halides with 6‐substituted imidazo[2,1‐b]thiazoles in the presence of bases proceeds regioselectively and affords 5‐phosphinoimidazo[2,1‐b]thiazoles, useful synthons for the preparation of various P(III) and P(V) derivatives. 5‐Phosphinoimidazo[2,1‐b]thiazoles are selectively alkylated at the phosphorus or heterocyclic nitrogen atom, depending on the alkylating agent. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:648–655, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20166     

CdBiO2Cl: synthesis and powder structure solution

The title compound, cadmium bismuth dioxide chloride, CdBiO₂Cl, was obtained as a white powder by reaction of solid BiOCl with CdO at 973 K. Ab initio crystal structure determination was carried out using X-ray powder diffraction techniques, including direct methods for atom location and Rietveld fitting for the final refinement. Being monoclinic, the crystal structure can be related to tetragonal Sillen layered phases. The main structural elements present are CdBiO₂⁺ pleated metal–oxy­gen layers alternating with Cl layers along the c axis, whereas along the b axis, all atoms are on mirror planes. The formation of a strong Cd—Cl bond draws the layers together, causing layer deformation and a monoclinic distortion in the layer arrangement.     

Exploration of the Crystal Structure and Thermal and Spectroscopic Properties of Monoclinic Praseodymium Sulfate Pr2(SO4)3

Praseodymium sulfate was obtained by the precipitation method and the crystal structure was determined by Rietveld analysis. Pr₂(SO₄)₃ is crystallized in the monoclinic structure, space group C2/c, with cell parameters a = 21.6052 (4), b = 6.7237 (1) and c = 6.9777 (1) Å, β = 107.9148 (7)°, Z = 4, V = 964.48 (3) ų (T = 150 °C). The thermal expansion of Pr₂(SO₄)₃ is strongly anisotropic. As was obtained by XRD measurements, all cell parameters are increased on heating. However, due to a strong increase of the monoclinic angle β, there is a direction of negative thermal expansion. In the argon atmosphere, Pr₂(SO₄)₃ is stable in the temperature range of T = 30–870 °C. The kinetics of the thermal decomposition process of praseodymium sulfate octahydrate Pr₂(SO₄)₃·8H₂O was studied as well. The vibrational properties of Pr₂(SO₄)₃ were examined by Raman and Fourier-transform infrared absorption spectroscopy methods. The band gap structure of Pr₂(SO₄)₃ was evaluated by ab initio calculations, and it was found that the valence band top is dominated by the p electrons of oxygen ions, while the conduction band bottom is formed by the d electrons of Pr³⁺ ions. The exact position of ZPL is determined via PL and PLE spectra at 77 K to be at 481 nm, and that enabled a correct assignment of luminescent bands. The maximum luminescent band in Pr₂(SO₄)₃ belongs to the ³P₀ → ³F₂ transition at 640 nm.     

Electronic structure of strongly correlated systems: recent developments in multiconfiguration pair-density functional theory and multiconfiguration nonclassical-energy functional theory

Strong electron correlation plays an important role in transition-metal and heavy-metal chemistry, magnetic molecules, bond breaking, biradicals, excited states, and many functional materials, but it provides a significant challenge for modern electronic structure theory. The treatment of strongly correlated systems usually requires a multireference method to adequately describe spin densities and near-degeneracy correlation. However, quantitative computation of dynamic correlation with multireference wave functions is often difficult or impractical. Multiconfiguration pair-density functional theory (MC-PDFT) provides a way to blend multiconfiguration wave function theory and density functional theory to quantitatively treat both near-degeneracy correlation and dynamic correlation in strongly correlated systems; it is more affordable than multireference perturbation theory, multireference configuration interaction, or multireference coupled cluster theory and more accurate for many properties than Kohn–Sham density functional theory. This perspective article provides a brief introduction to strongly correlated systems and previously reviewed progress on MC-PDFT followed by a discussion of several recent developments and applications of MC-PDFT and related methods, including localized-active-space MC-PDFT, generalized active-space MC-PDFT, density-matrix-renormalization-group MC-PDFT, hybrid MC-PDFT, multistate MC-PDFT, spin–orbit coupling, analytic gradients, and dipole moments. We also review the more recently introduced multiconfiguration nonclassical-energy functional theory (MC-NEFT), which is like MC-PDFT but allows for other ingredients in the nonclassical-energy functional. We discuss two new kinds of MC-NEFT methods, namely multiconfiguration density coherence functional theory and machine-learned functionals.

This feature article overviews recent work on active spaces, matrix product reference states, treatment of quasidegeneracy, hybrid theory, density-coherence functionals, machine-learned functionals, spin–orbit coupling, gradients, and dipole moments.     

A Comprehensive Study of N-Butyl-1H-Benzimidazole

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1–C2) is distributed into antibonding σ* (C1–C6), σ* (C1–N26), and σ* (C6–H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra.     

An Efficient Method of Birch Ethanol Lignin Sulfation with a Sulfaic Acid-Urea Mixture

For the first time, the process of birch ethanol lignin sulfation with a sulfamic acid-urea mixture in a 1,4-dioxane medium was optimized experimentally and numerically. The high yield of the sulfated ethanol lignin (more than 96%) and containing 7.1 and 7.9 wt % of sulfur was produced at process temperatures of 80 and 90 °C for 3 h. The sample with the highest sulfur content (8.1 wt %) was obtained at a temperature of 100 °C for 2 h. The structure and molecular weight distribution of the sulfated birch ethanol lignin was established by FTIR, 2D ¹H and ¹³C NMR spectroscopy, and gel permeation chromatography. The introduction of sulfate groups into the lignin structure was confirmed by FTIR by the appearance of absorption bands characteristic of the vibrations of sulfate group bonds. According to 2D NMR spectroscopy data, both the alcohol and phenolic hydroxyl groups of the ethanol lignin were subjected to sulfation. The sulfated birch ethanol lignin with a weight average molecular weight of 7.6 kDa and a polydispersity index of 1.81 was obtained under the optimum process conditions. Differences in the structure of the phenylpropane units of birch ethanol lignin (syringyl-type predominates) and abies ethanol lignin (guaiacyl-type predominates) was manifested in the fact that the sulfation of the former proceeds more completely at moderate temperatures than the latter. In contrast to sulfated abies ethanol lignin, the sulfated birch ethanol lignin had a bimodal and wider molecular weight distribution, as well as less thermal stability. The introduction of sulfate groups into ethanol lignin reduced its thermal stability.