Crystal Structure Dynamics: Evidence by Diffraction and Spectroscopy

Bragg diffraction is a major tool to solve and refine crystal structures, though it is limited as results obtained from the bulk sample are averaged in time and space. In contrast, spectroscopy is site sensitive, and thus a probe for local structure with high time and space resolution. Combination of both methods may reveal important additional information on crystal structures such as disorder and dynamics, and may even help avoid pitfalls in structure solution. Among the given examples are three minerals, i.e., lawsonite, hemimorphite, leonite, which show phase transitions from dynamically disordered to ordered structures. Continuous evolution from order to dynamic disorder, however without a phase transition, is found in washing soda. Finally, examples of proton dynamics in a tetragonal garnet and in minerals with very strong hydrogen bonds are presented

Synthesis, crystal structure and biological activity of copper(II) complex with 4-nitro-3-pyrazolecarboxylic ligand

The reaction of 4-nitro-3-pyrazolecarboxylic acid and Cu(OAc)2⋅H2O in ethanol resulted in a new coordination compound [Cu2(4-nitro-3- -pzc)2(H2O)6]2H2O (4nitro-3pzc = 4-nitro-3-pyrazolecarboxylate). The compound was investigated by means of single-crystal X-ray diffraction and infrared spectroscopy. The biological activity of the complex was also tested. In the crystal structure of [Cu2(4nitro-3-pzc)2(H2O)6]2H2O, the Cu(II) ion is in a distorted [4+2] octahedral coordination due to the Jan–Teller effect. A survey of the Cambridge Structural Database showed that the octahedral coordination geometry is generally rare for pyrazole-bridged Cu(II) complexes. In the case of Cu(II) complexes with the 3-pyrazolecarboxylato ligands, no complexes with a similar octahedral coordination geometry have been reported. Biological research based on determination of the inhibition effect of the commercial fungicide Cabrio top and the newly synthesized complex on Ph. viticola were performed using the phytosanitary method

The crystal structure of bis[4-bromo-2-(1H-pyrazol-3-yl) phenolato-κ2N,O] copper(II), C18H12Br2CuN4O2

C 18 H 12 Br 2 CuN 4 O 2 , monoclinic, P 2 1 / c (no. 14), a  = 11.5165(11) Å, b  = 5.4369(5) Å, c  = 14.4872(14) Å, V  = 873.52(14) Å 3 , Z  = 2, R gt ( F ) = 0.0232, wR ref ( F 2 ) = 0.0559, T  = 200 K

Crystal structure of ethyl 3-(trifluoromethyl)-1H-pyrazole-4-carboxylate, C7H7F3N2O2

C7H7F3N2O2, monoclinic, P21/m (no. 11), a = 6.8088(8) Å, b = 6.7699(9) Å, c = 9.9351(12) Å, β = 105.416(3)°, V = 441.48(9) Å 3 , Z = 2, R gt ( F ) = 0.0398, wR ref ( F 2 ) = 0.1192, T = 200(2) K

FTIR spectroscopy of lawsonite between 82 and 325 K

Lawsonite single crystals were investigated by polarized FfIR spectroscopy at wave numbers between 8000 and 1000 cm^(-1) and temperatures between 82 and 325 K. This temperature range contains three lawsonite phases-Cmcm > 273 K, 273 K > Pmcn > 150 K, P2_1cn < 150 K-which are characterized by different rotations of hydroxyl groups and H20 molecules. Unlike previous studies of H_2O in minerals, which assumed weakly bonded, symmetric H_2O molecules, the highly asymmetric H_2O molecule in lawsonite required a modified approach that uses the single, uncoupled O-H stretching frequencies and orientations of the individual OH groups in the H_2O molecule. The formation of a strong hydrogen-bond system with decreasing temperature is characterized by a shift of O-H stretching bands from 2968 and 3252 cm^(-1) at 325 K to 2817 and 3175 cm^(-1) at 82 K. These frequencies are in good agreement with the corresponding hydrogen-bond lengths (H...O = 1.66 and 1.74 Å, O-H...O = 2.60 and 2.66 Å) at low temperatures. The orientations of the O-H vectors determined from polarized IR measurements also confirm the H-atom positions refined from previous X-ray structure determinations at low temperatures. However, the disagreement between spectroscopically determined distances (and orientations) and those from X-ray refinements at ambient conditions indicates that the room-temperature Cmcm structure of lawsonite contains dynamically disordered hydroxyl groups and H_2O molecules. The smooth changes of stretching and bending frequencies across the phase boundaries at 273 and 150 K also suggest that the lawsonite phase transitions are of a dynamic order-disorder type rather than a displacive type. Deuteration experiments on differently oriented, single-crystal lawsonite slabs at 350 ºC and 1.2-2.5 kbar showed that lawsonite has a preferred H-diffusion direction parallel to [001]. This is consistent with the crystal structure showing channels parallel to [001], which are solely occupied by H atoms. The spectra of isotopically diluted samples, which are almost identical to those of natural lawsonite, indicate that band-coupling effects are generally weak. The FTIR powder spectra of the lawsonite-type mineral hennomartinite, Sr-Mn_2[Si_2O_7](OH)_2.H_2O, are similar to the lawsonite Z spectra and confirm the existence of both strong and weak hydrogen bonds in its structure

An IR absorption calibration for water in minerals

Using IR absorption data from polarized measurements on single-crystal minerals with stoichiometric water contents (in the form of H_(2)O or OH groups in the structure), a linear calibration curve (r^2 nearly equal 0.98) for water in minerals is established in the form: epsilon i , (the integrated molar absorption coefficient in units of cm^(-2) per mol H_(2)O/L) = 246.6(3753 - upsilon ) (upsilon = the mean wavenumber of the OH stretching band [in cm^(-1)]). The investigated minerals include hydrogrossular, analcime, hemimorphite and its dehydrated phase, lawsonite, goethite, diaspore, manganite, mozartite, and pectolite. The influence of hydrogen bonding, leading to increased absorption values with lower OH stretching band energies, is confirmed. It is further shown that only the use of integrated absorbance values (band areas) results in a linear correlation with water content, whereas linear absorption data (peak heights) are not correlated. The calibration agrees with previously published quantitative IR data on staurolite and trace H in pyroxenes. It is also close to the frequently used trend of Paterson (1982). However, some of the previous calibrations of trace H in nominally anhydrous minerals, e.g., kyanite and pyrope, differ appreciably from the correlation derived from stoichiometrically hydrous minerals

IR spectroscopy of hemimorphite between 82 and 373 K and optical evidence for a low-temperature phase transition

Polarized IR absorption spectra of oriented hemimorphite single-crystals were recorded in the region of the O-H fundamentals and combination bands between 82 and 373 K. The almost exclusive orientation of the absorption bands in the (010) plane is in agreement with previous neutron structure refinements. The weak H bonds of the OH groups and water molecules are confirmed by the energies of the OH stretching fundamentals around 3350-3600 cm^(-1). However, even though two O-H stretching bands in both ɑ and c are predicted by factor group analysis, three strong bands in ɑ, and two in c are observed. This fact, as well as the occurrence of weak satellite bands in the a and c spectra, and a minor component parallel to the b axis direction, indicate complicated dynamics of the water molecules and OH groups within the structural channels. These motions can be partly explained by a twisting motion of the water molecule around its two-fold molecular axis. A much better interpretation for these motions, however, is found in dynamic proton disorder, which describes a hopping motion between disordered proton sites. A possible dynamic disorder-order phase transition at low temperatures was tested by determination of birefringence values (Δn) of hemimorphite between 82 and 373 K. A strong discontinuity in the slope of Δn_(x,γ) and Δn_(γ,z) was observed at 98(2) K. This, together with considerable energy shifts of IR bands upon cooling, provides evidence for a low-temperature second-order phase transition in hemimorphite