Investigation of lignin models of the biphenyl type by X-ray crystallography and NMR spectroscopy

Lignin models of the biphenyl type have been synthesized and crystal structures of two of them have been determined. The tetraacetate of 5,5-bis(hydroxymethyl)-3,3-dimethoxy-2,2-biphenyldiol crystallizes in space group witha=11.319(2),b=12.232(6),c=9.242(3) Å, =101.66(3)°, =108.14(2)°, =79.08(2)° andZ=2.R=0.036 (2720 observed [I>3(I)] reflections). The acetate of 5,5-di-tert-butyl-2,3,3-trimethoxy-2-biphenylol crystallizes in space group witha=11.972(2),b=21.621(3),c=9.834(1) Å, =91.18(1)°, =113.13(1)°. =98.42(1)°, andZ=4.R=0.050 (8129 observed [I>3(I)] reflections).¹H NMR and¹³C NMR data for the above-mentioned compounds and a third model, the diacetate of 5,5-bis(1-hydroxyethyl)-2,2,3,3-tetramethoxybiphenyl, are reported. Observed signal positions are compared with those calculated on the basis of crystal structure data. The possibilities to obtain structural information about biphenyl structures in lignins from NMR spectra are discussed.     

Investigation of 2-(3,4-dimethoxyphenyl)-5,6-dimethoxy-1H-indene by X-ray crystallography and NMR spectroscopy

2-(3,4-Dimethoxyphenyl)-5,6-dimethoxy-1H-indene (obtained by acid treatment of 1,2-bis(3,4-dimethoxyphenyl)-1,3-propanediol) crystallizes in space groupP2₁/c witha=6.836(6),b=28.631(9),c=16.344(6) Å, =95.73(5)°, andZ=8. There are two molecules in the asymmetric unit; the conformations of these molecules exhibit minor differences. In the crystals the double bond in the five-membered ring of the compound is disordered over two positions. The nature of the bonds in the five-membered ring could be ensured by¹H-NMR and¹³C-NMR spectral examinations.     

Structures of nitroso- and nitroguanidine X-ray crystallography and computational analysis

The X-ray structures of solid nitroguanidine (ngoH):orthorhombic, Fdd2, a = 17.6181(14), b = 24.848(2), c = 3.5901(4) Å, V = 1571.7(3) ų, Z = 16 and nitrosoguanidine (ngH); monoclinic, P 2₁/n, a = 3.64510(10), b = 11.746(2), c = 8.6483(14) Å, = 99.167(2), V = 365.55(9) ų, Z = 4 have been determined utilizing single crystal X-ray diffraction methods. The results are compared with the most stable gaseous configurations derived from ab inito calculations. The lowest energy calculated configuration for the ligands and experimentally observed crystal structures are in excellent agreement. In the solid state, both the ngoH and ngH contain discrete molecules in their unit cells which are planar (within experimental error), in the diamine configurations and are structurally identical except for an oxygen atom. In solid ngH, two ligand molecules have four nitrogen atoms arranged in a plane such that they are suitable for coordination to a nickel ion (1.945, 2.064 Å), when it is at the 1/2, 1/2, 1/2 unit-cell position giving the observed complex. As far as we are aware, this is the first instance in which a ligand crystal structure is essentially the same, with minor distance, angle and torsion angle changes, as the complex it forms and suggests some potentially unique properties and applications for this material.     

Synthesis and X-ray crystallography of cholest-3,5-diene-7-one-oxime

Cholest-3,5-diene-7-one-oxime (C₂₇H₄₃NO) was prepared using a usual synthetic route and its three-dimensional structure was determined by X-ray diffraction methods. The transparent platelike crystals of this compound crystallized in the monoclinic space group P2₁, with unit cell parameters a = 14.302(2) Å, b = 11.475(2) Å, c = 15.919(4) Å, = 106.04(1)°, (Cu K) = 1.5418 Å, Z = 4. The structure was solved by direct methods and refined to an R-value of 0.075 for 4640 observed reflections. Two crystallographically independent molecules were observed in the asymmetric unit cell. The ring A in both the molecules was found to exist in 1,10 half-chair conformation while ring C in chair conformation. The rings B and D in both the molecules adopted different conformations. Three intermolecular interactions of the type C–H O and C–H N were also observed.     

Synthesis and X-ray Structure of Acetoxy-4-methyl Phenyl Methyl Acetate

Abstract  

The title compound belongs to acylal class of organic materials and it crystallizes in the monoclinic space group P2₁/c with unit cell parameters a = 7.643(2) ?, b = 20.546(6) ?, c = 7.783 ?, β = 112.206(2)°, V = 1131.50(5) ?³ and Z = 4. The structure has been solved by direct methods and the final R-factor is 0.0401 for 2579 unique reflections. The acetate groups are deviated significantly from the plane of phenyl ring atoms. There are two C–H···O intermolecular hydrogen bonds which gives rise to an antiparallel dimer pattern.     

Structure of 4-(2-chloro-4,5-dimethoxybenzylidene)-2-methyl-5-oxazolone. X-ray and NMR study

The azlactone of 6-chloroveratraldehyde 3 (4-(2-chloro-4,5-dimethoxybenzylidene)-2-methyl-5-oxazolone) was synthesized from 6-chloroveratraldehyde 2 and its structure investigated using X-ray crystallographic and nuclear magnetic resonance methods. Compound 3 crystallized in the P2₁/c (#14) space group (Z = 4) with cell dimensions a = 9.148(2), b = 22.938(2), c = 6.707(1) Å, and = 111.50(2)°. The X-ray study shows that azlactone 3 exists as the Z-isomer and crystallizes as a planar structure, i.e., both the phenyl and azlactone ring systems, as well as the functional groups attached to them, lie in the same plane. The ¹H and ¹³C NMR spectral values also support the formation of the Z-isomer only, during the synthesis of 4-(2-chloro-4,5-dimethoxybenzylidene)-2-methyl-5-oxazolone.     

Investigation of an inclusion compound of trans-1,3-bis(3,4-dimethoxyphenyl)-2,3-epoxy-1-propanone with chloroform by NMR spectroscopy and X-ray crystallography

trans-1,3-Bis(3,4-dimethoxyphenyl)-2,3-epoxy-1-propanone crystallizes in a monoclinic form (m.p. 155–156°C, from ethanol) and a trigonal form (m.p. 125–126°C, from chloroform/hexane or chloroform). NMR studies revealed that chloroform is present in the crystals of the trigonal form (epoxide/chloroform ratio 3:1). Solid-state NMR experiments showed that the trigonal form was gradually converted into the monoclinic form on storage in vacuo. On the basis of NMR and X-ray examinations it was concluded that the trigonal form is an inclusion compound of trans-1,3-bis(3,4-dimethoxyphenyl)-2,3-epoxy-1-propanone with chloroform. The crystal structure of the trigonal form with space group of R , a = 36.0354(4), c = 8.2743(2) Å, and Z = 18, has been refined to R = 0.0506 by the employment of the SQUEEZE procedure implemented in PLATON-94.     

X-ray structure and NMR assignment of 3,4-dimethylthioquinoline

The title compound (C₁₁H₁₁NS₂) is monoclinic:P2₁/c,a=15.200(4),b=14.644(4),c=10.098(3),Z=8. The structure was solved by direct methods, and refined to anR value of 0.047 with 2886 independent reflections. There are two nonequivalent molecules in the unit cell. BothS-methyl groups have different spatial orientation: the-methyl group side-chain is approximately coplanar with the pyridine ring and turned to the ortho-position, but -methyl group side-chain is turned over this ring. Both¹H and¹³C NMR spectra were assigned using 1D and 2D experiments. The NOE measurements are consistent with inter-proton distances from X-ray data.Part XV in the series of Azinyl sulfides.     

The crystal structure of Zr2Se reinvestigated by electron crystallography and X-ray powder diffraction

The metal-rich compound Zr₂Se is of particular interest for electron crystallography, since it was one of the first examples that proved that heavy-atom structures can be solved via quasi-automatic direct methods from selected area electron diffraction intensities [1]. For this reason, Zr₂Se has been chosen as a model to discuss the possibilities and the limits of the quasi-kinematical approach that has been successfully used to determine this and related structures from high-resolution electron microscopy (HREM) images and selected area electron diffraction. In order to quantify the achievable accuracy of the electron crystallography techniques used, the corresponding structures are compared with results from structural analysis with X-ray powder data and with a model received from first-principles calculations. The latter structure was chosen in this study as a reference, since the calculations do not depend on experimental parameters. Analysis of the obtained result from electron diffraction structural analysis (EDSA) shows that the structural model is, on average, only off by 0.08 Å, despite the investigated crystal having an effective thickness of 286 Å. The corresponding result from Rietveld refinement with X-ray powder data agrees to within 0.04 Å with the structure from calculation and within 0.03 Å with the result from an earlier single crystal X-ray study [2].     

Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through S_N2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.     

Preparation and NMR studies of cesium hydroselenite

This work is a part of the systematic study of the structure and the physical properties of alkaline hydroselenite crystals with the general formula MeHSeO₃, where Me is an alkali ion. The characteristic feature of this family is a net of hydrogen bonds between SeO₃ groups forming closed [HSeO ₃ ^? ]₂ dimers.     

X-ray studies of thermal expansion and phase transitions in (NH4)2SbF5 crystals

X-ray diffraction studies of phase transitions in (NH₄)₂SbF₃ single crystals have been made by using the Bond-type diffractometer for high-precision measurements of the unit-cell dimensions in a function of temperature. The principal linear thermal expansion coefficients and the linear Eulerian strain tensor have been calculated in the temperature interval 110 – 298 K. The phase transition diagram was proposed and the sequence of the phases has been compared with the results of other experimental techniques (NMR, NQR, DTA, electrophysical methods).     

NMR and X-ray Investigations of a Plastic Crystalline Phase in MBBA

Abstract

Wideline and high resolution NMR studies have been carried out on MBBA in its isotropic, nematic and solid phases. Isotropic and nematic phase spectra correspond to what has been reported earlier. In the solid phase, contrary to expectations, very intense narrow signals similar to signals of the isotropic phase have been observed for the first time at temperatures close to the solid ? nematic phase transition temperature. This indicates rapid reorientational or translational motion in the system. The X-ray results however confirm the existence of translational order. The results are interpreted as indicative of the existence of a plastic crystalline phase in MBBA.     

Structure,IR, and NMR spectra of tetrakis(4-methyl piperidinedithiocarbamate) dimercury(II)

The compound C₁₄H₂₄HgN₂S₄ was prepared and characterized by means of X-ray, IR, and NMR measurements. The crystals are monoclinic, space group P2₁/c, (No. 14) witha=8.697(2),b=19.156(3),c=12.098(2) Å,=108.14(1)° andZ=4. The structure was solved by the heavy-atom method, and least-squares refinement of structural parameters led to a conventionalR factor of 0.027 for 2469 independent reflections. The structure consists of discrete dimeric units with the metals coordinated to five sulphur atoms. The IR and NMR spectra are discussed on the basis of the known structure.     

The crystal and solution structure of 2,4-dinitrophenyl phenylsulfide determined by X-ray crystallography and13C-NMR spin-lattice relaxation measurements

The crystal structure of 2,4-dinitrophenyl phenylsulfide, C₁₂H₈N₂O₄S, has been determined by single crystal X-ray diffraction. The crystals are monoclinic, space groupP2 _{1/n, Z} = 8, witha = 10.670(2),b = 8.381(4),c = 27.998(18) Å, and = 100.44(4) °. There are two crystallographically independent molecules per asymmetric unit. All intensity measurements were made at room temperature on an Enraf-Nonius CAD-4 automatic diffractometer using monochromatized MoK radiation. The structure was solved by direct methods and refined to a finalR value of 0.032. The two independent molecules have nearly identical geometries, with the most notable difference being the torsion angles involving the sulfur atoms. Thepara-nitro groups are more nearly in the planes of the central phenyl rings than are theortho-nitro groups although there may be nonbonded attractions between the latter. The two phenyls of each molecule are nearly at right angles to each other, as necessitated by steric forces involvingortho hydrogens. The characteristic distortions of the central phenyl rings caused by differing substituent electronegativities and degrees of conjugation are noted. The¹³C-NMR spectrum of the compound was assigned by comparison of calculated with observed chemical shift data. Calculated chemical shifts were obtained by incrementation of the chemical shifts of diphenylsulfide with standard nitro group additivities which were adjusted for the sulfur-nitro group interaction. Where necessary, assignments were confirmed with selective excitation spin-coupled subspectra. Solution behavior of the molecule was determined from spin-lattice (T ₁) relaxation measurements which showed the unsubstituted ring to reorient anisotropically about the C(21)-C(24) bond axis while the substituted ring appears to be governed by the overall isotropic reorientation of the molecular framework, indicating that the sulfur-nitro group interaction restricts anisotropic reorientation about the C(11)-C(14) bond axis.     

Neutron and X-ray scattering studies of Li2O–TeO2–V2O5 glasses

Neutron and X-ray scattering studies of (Li₂O)_x–(TeO₂)₂–V₂O₅ glasses with x = 0, 1 and 2, obtained by melting and subsequent cooling in air to room temperature, have been performed. Reciprocal space data have been Fourier transformed into real space yielding the radial distribution functions. Nearest and next neighbor peaks have been analyzed using a least-squares fitting method which suggests the presence of both TeO₃ and TeO₄ coordination polyhedra, the fivefold coordination of lithium and mixture of 6, 5 and 4 coordination numbers of vanadium. These results are discussed in relation to the electronic and ionic conductivity properties.