Lattice vibrations of the molecular crystal of photoreactive substance with defects

Lattice vibrations are studied theoretically by density-functional based tight-binding methods for the model structure of 2-(2'-hydroxyphenyl)benzoxazole crystal with defects. 2-(2'-hydroxyphenyl)benzoxazole is a photoreactive compound that exhibits excited state intramolecular proton transfer in the structure with an OH...N hydrogen bond. The unit cell of the model structure consists of two crystal unit cells where the molecules have the structure with intramolecular hydrogen bonds OH...N and one molecule is supposed to have a different orientation of the whole molecule or its fragment. The different orientation of the fragment forms the structure with an intramolecular hydrogen bond OH...O. It is calculated that defect caused by the different orientation of the molecule have a lower energy than the defect caused by the different orientation of the fragment. In the frequency region where the contribution of external vibrations of the molecules is significant, the vibrations mainly involve several molecules in the cell. In the region of internal vibrations there are modes, which are local vibrations of the defects. These local vibrations involve mainly motion of the atoms constituting the defect molecule. The number of local vibrations is larger for the defect that corresponds to the formation of the structure with the OH...O hydrogen bond than for the defect that corresponds to the different orientation of the whole molecule with the OH...N hydrogen bond. The internal vibrations of the defect molecule formed by the different orientation of phenol fragment in the lattice undergoes frequency shift in relation to the frequency of the modes of isolated molecule.

Lattice vibrations and disorder in crystalline benzoxazoles undergoing excited state intramolecular proton transfer: DFTB modeling

Structure and crystal lattice vibrations are calculated for 2-(2'-hydroxyphenyl)bezoxazole and bis-(2,5-benzoxazolyl)hydroquinone by density functional based tight-binding methods. Despite lowering of the molecular symmetry, structure parameters of the molecules in crystal and forms of the internal vibrations are similar to those of isolated molecules. Weak interaction between the molecules in the molecular crystals leads to appearance of the external vibrations, splitting and mixing of the vibrations of the isolated molecules into internal crystal vibrations. External and internal vibrations are not separated well; contribution of the translations and librations is noticeable in the region below 150 cm-1. The magnitude ofthe splitting does not exceed 4 cm-1 for the most vibrations. The internal vibrations that correspond to the out-of plane molecular vibrations demonstrate larger molecule-to-crystal frequency shift than in-plane modes, mostly to higher frequencies, whereas the modes involving torsion motion of the OH bond are shifted toward lower frequencies. Mixing occurs for the molecular vibrations with frequencies that are different by less than 16 cm-1. Calculations performed for model molecular clusters show that the defectcaused by different molecule orientation has lower energy than the defect related to the formation ofrotamers.

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules.

Correction: Water-mediated long-range interactions between the internal vibrations of remote proteins

Correction for ‘Water-mediated long-range interactions between the internal vibrations of remote proteins’ by Anna Kuffel et al., Phys. Chem. Chem. Phys., 2015, 17, 6728–6733.

Kerimasite, {Ca3}[Zr2](SiFe3+2)O12 garnet from the Vysoká-Zlatno skarn, Štiavnica stratovolcano, Slovakia

Kerimasite {Ca3}[Zr2](SiFe23+)O12, a rare member of the garnet supergroup, has been identified in association with andradite–grossular and their hydrated analogues, monticellite, perovskite, clintonite, anhydrite, hydroxylellestadite–fluorellestadite, spinel, magnetite, brucite, valeriite and other minerals from a Ca-Mg skarn in the exocontact of a granodiorite porphyry intrusion in Vysoká-Zlatno Cu-Au skarn-porphyry deposit, the Štiavnica stratovolcano, Central Slovakia. Kerimasite forms euhedral-to-anhedral crystals, 2 to 100 μm across with 0.73–1.62 atoms per formula unit (a.p.f.u.) Zr (16.2–33.6 wt.% ZrO2), 0.34–0.66 a.p.f.u. Ti (4.6–9.3 wt.% TiO2), 0.01 to 0.05 a.p.f.u. Hf (0.4–1.7 wt.% HfO2: the largest Hf content reported in kerimasite), and small amounts of Sn, Sc and Nb (≤0.02 a.p.f.u.). Tetrahedral Si (0.99–1.67 a.p.f.u.; 9.8–18.1 wt.% SiO2) is balanced by 0.85–1.26 a.p.f.u. Fe3+ and by 0.46–0.76 a.p.f.u. Al. The crystals commonly show regular, oscillatory concentric zoning or irregular patchy internal textures due to Zr, Ti, Fe, Al and Si variations during growth or partial alteration and dissolution-reprecipitation. The main substitutions in kerimasite are Y(Fe,Sc)3+ + ZSi4+ = Y(Zr,Ti,Hf,Sn)4+ + Z(Fe,Al)3+ and Ti4+ = Zr4+. Associated andradite locally contains irregular Ti- and Zr-rich zones with ≤11 wt.% TiO2 and ≤4.4 wt.% ZrO2. In comparison with common Ca-rich garnets, the micro-Raman spectrum of kerimasite shows that many bands shift towards much lower wavenumbers, either due to Fe3+ substitution on the Z site or to the strong influence of neighbouring octahedrally-coordinated Zr4+ on internal vibrations of tetrahedra that share oxygens. The formation of kerimasite, monticellite, perovskite and other phases indicate a relatively Ca-rich and Si, Al-poor environment, analogous to other known occurrences of Ca-Zr garnets (Ca-rich skarns and xenoliths, carbonatites). Kerimasite and associated skarn minerals originated during contact-thermal metamorphism of Upper Triassic marl slates with limestone, dolomite, anhydrite and gypsum by Miocene granodiorite porphyry at T ≈ 700°C and P ≈ 50–70 MPa.

Water-mediated long-range interactions between the internal vibrations of remote proteins

We demonstrated that interfacial water can influence and mediate long-range protein–protein interactions leading to a partial synchronization of internal movements of proteins.

Investigations of the Fe sulfosalts berthierite, garavellite, arsenopyrite and gudmundite by Raman spectroscopy

Arsenopyrite (FeAsS), gudmundite (FeSbS) and the rarer Fe sulfosalts berthierite (FeSb2S4) and garavellite (FeSbBiS4), were investigated by Raman spectroscopy. Whereas (Sb,Bi)S3 pyramids are responsible for the Raman spectra of berthierite and garavellite, the spectra of gudmundite and arsenopyrite arise from the stretching and bending modes of (Sb,As)S units. Internal vibrations for berthierite and garavellite occur between 400 and 50 cm–1, and those of the gudmundite and arsenopyrite between 500 and 100 cm–1. The longer bond distances of the SbS3 groups readily explain the lower frequencies for berthierite in comparison with garavellite. Similarly, the greater mass and the longer bond distances of the Sb–S units also explain the lower frequencies observed for gudmundite relative to arsenopyrite.