A. T. H. Lenstra

Solids modeled by abinitio crystal field methods. X. Structure of α‐glycine, β‐glycine, and γ‐glycine using a 15‐molecule cluster

The structure of three polymorphic forms of glycine in the crystal phase, α‐glycine (P21/n), β‐glycine (P21), and γ‐glycine (P32), was completely optimized with standard gradient procedures using a point charge model and using a model constituted of a 15‐molecule cluster surrounded by point charges. The calculations were performed with a 6‐31G basis set and in the SCF step of the calculations the MIA approach was used. The results for the 15‐molecule cluster are in better agreement with the experimental results than the results obtained with the point charge model.

Derivatives of 1-phenyl-3-methylpyrazol-2-in-5-thione and their oxygen analogues in the crystalline phase and their tautomeric transformations in solutions and in the gas phase

Abstract 1-Phenyl-3-methylpyrazol-2-in-5-thione, crystallised from methanol, was shown to exist in the tautomeric NH-form, stabilised by intermolecular NH⋯S hydrogen bonds. In solutions, however, the molecule is found predominantly as the SH-tautomer, accompanied (in low-polar solvents) by a small amount of the CH-tautomer. 1-Phenyl-3-methyl-4-benzoylpyrazol-2-in-5-thione occurs in the crystal as well as in solution in the SH-tautomeric form, stabilised by an intramolecular SH⋯O bridge. In dimethylsulfoxide solution indications were found for an additional SH-tautomer in a conformation lacking the intramolecular H-bridge. The structure of 1-phenyl-3-methylpyrazol-2-in-5-one was redetermined by X-ray single crystal diffraction at 120°K in order to obtain more accurate geometry and hydrogen bonding parameters.

Copper(II) and zinc(II) co-ordination compounds of tridentate bis(benzimidazole)pyridine ligands. Crystal and molecular structures of bis[2,6-bis(1′-methylbenzimidazol-2′-yl)pyridine]copper(II) diperchlorate monohydrate and (acetonitrile)[2,6-bis(benzimidazol-2′-yl)pyridine](perchlorato)copper(II) perchlorate

Compounds are described of general formulae Cu(L1)X2, Cu(L1)2X2, Cu(L2)X2, and Cu(L2)2X2 with L1= 2,6-bis(benzimidazol-2′-yl)pyridine, L2= 2,6-bis(1′-methylbenzimidazol-2′-yl)pyridine, and X = Cl, Br, or ClO4. For comparison also a few zinc(II) halides were prepared and characterized. The compounds were structurally characterized by i.r., ligand-field, and e.s.r. spectra and for two representative cases [Cu(L1)(CH3CN)(ClO4)][ClO4](1) and [Cu(L2)2][ClO4]2·H2O (2) also by X-ray diffraction techniques. Compound (1) crystallizes in space group P21/c with a= 14.061(1), b= 20.638(1), c= 8.273(1)A, β= 101.119(8), and Z= 4; R= 0.0366 for 4 265 observed reflections with I > 2σ(I). Compound (2) crystallizes in space group P21/c with a= 8.4824(22), b= 29.1965(29), c= 16.7393(24)A, β= 95.836(17)°, and Z= 4; R= 0.062 for 3 165 observed reflections with I > 3σ(I). The structure of (1) consists of one tridentate chelating L1 ligand and CH3CN, co-ordinated in a square-planar geometry (Cu–N 1.96–2.03 A) with a perchlorato oxygen at 2.40 A, thereby completing a five-co-ordinate geometry. A sixth ligand at 2.8 A(from another perchlorate oxygen) is considered to be semico-ordinating. The structure of (2) consists of one tridentate and one bidentate L2, chelating in a five-co-ordinate geometry, again tetragonal pyramidal, with the apical ligand (Cu–N 2.51 A) coming from the bidentate chelating L2. The sixth donor atom, again from a perchlorate oxygen, at 2.70 A is considered to be semi-co-ordinating. Spectroscopic and magnetic data have been used to deduce structures for the other copper(II) compounds based on these two X-ray structures.

An ab initio study of crystal field effects, part 3: Solid- and gas-phase geometry of formamide, modeling the changes in a peptide group due to hydrogen bonds

A model of the solid state of formamide is constructed by optimizing a central molecule in an electrostatic field of the proper symmetry. Attention is paid to the way the electrostatic charges are obtained. Point charges obtained from a Mulliken population analysis yield a final set of atomic charges in the central molecule that agree reasonably well with those obtained experimentally after ak-refinement of formamide. Point charges from a so-called stockholder partitioning agree slightly less. Furthermore, the simple crystal field adaptation of standard ab initio methods reproduces within experimental limits the differences in C=O and C-N lengths, observed between the gas-phase and the solid state geometry. Again, a Mulliken field agrees slightly better than a stockholder field, but the difference in performance is statistically insignificant. In a survey of 221 high-quality single-crystal x-ray determinations of compounds containing the peptide group N-C=O, we found evidence supporting quantitatively the conclusion that the increase of C=O and the decrease of C-N bond length in the gas-to-solid transition is dominated by the effects of hydrogen bonding. It was shown that the C=O bond lengthens by about 0.011 å per H-bond it accepts, while the N-C bond diminishes by about 0.015 å per H-bond it donates.

Structures of copper(II) and manganese(II) di(hydrogen malonate) dihydrate; effects of intensity profile truncation and background modelling on structure models

The crystal structures of the title compounds were determined with net intensities I derived via the background-peak-background procedure. Least-squares optimizations reveal differences between the low-order (0 < s < 0.7 A(-1)) and high-order (0.7 < s < 1.0 A(-1)) structure models. The scale factors indicate discrepancies of up to 10% between the low-order and high-order reflection intensities. This observation is compound independent. It reflects the scan-angle-induced truncation error, because the applied scan angle (0.8 + 2.0 tan theta) degrees underestimates the wavelength dispersion in the monochromated X-ray beam. The observed crystal structures show pseudo-I-centred sublattices for three of its non-H atoms in the asymmetric unit. Our selection of observed intensities (I > 3 sigma) stresses that pseudo-symmetry. Model refinements on individual data sets with (h + k + l) = 2n and (h + k + l) = 2n + 1 illustrate the lack of model robustness caused by that pseudo-symmetry. To obtain a better balanced data set and thus a more robust structure we decided to exploit background modelling. We described the background intensities B(H-->) with an 11th degree polynomial in straight theta. This function predicts the local background b at each position H--> and defines the counting statistical distribution P(B), in which b serves as average and variance. The observation R defines P(R). This leads to P(I) = P(R)/P(B) and thus I = R - b and sigma(2)(I) = I so that the error sigma(I) is background independent. Within this framework we reanalysed the structure of the copper(II) derivative. Background modelling resulted in a structure model with an improved internal consistency. At the same time the unweighted R value based on all observations decreased from 10.6 to 8.4%. A redetermination of the structure at 120 K concluded the analysis.

Synthesis, spectroscopy and thermal properties of the nickel(II), palladium(II) and copper(II) complexes of bis(aminoalkyl)-oxamides (= LH2) including the crystal structure of Cu2L(NO3)2

SummaryThe synthesis of the NiII, PdII and CuII complexes of N, N′-bis(aminoalkyl)oxamides (LH2) is described and structures are proposed on the basis of their physical and spectroscopic properties. With NiII and PdII only one complex is formed with general formula NiL or PdL, characterised by coordination through two deprotonated amide N-atoms and two terminal NH2 groups. With CuII it proved possible to obtain three structurally different compounds, depending on the pH, with general formulae Cu(LH2)X2, Cu2(L)X2 and CuL in which X=Cl, Br or NO3. The structure of [Cu2(C8O2N4H16](NO3)2 was solved by means ofx-ray diffraction; Mr=451.33, monoclinic, space group P21/n, a=9.503(4), b=7.614(1), c=10.407(3) Å, β=98.43(3)°, V=744.3(7)Å3, Z=2, Dx=1.202 g cm−3, μ=1.33 cm−1, γ(MoKα)=0.71073 Å, F(000)=520, room temperature, R=0.043, wR=0.047 for 1080 observed [I>-3σ(I)] not systematically absent reflections out of 1423 measurements and 137 variables. The compound has a conformational chair/boat disorder with 82% in the more stable chair form.

The effect of non-bonded attractive electronic (anomeric) interactions on conformation and geometry of organic phosphates and thiophosphates

Abstract Substituted 1,3,2-dioxaphosphorinane-2-oxides and -2-sulfides are classified according to the conformation of the ring and the orientation (axial or equatorial) of the P=O/P=S bond. Geometrical parameters (torsion angles, valence angles and bond lengths) of 37 compounds are analyzed and several systematic class differences are observed. The anomeric effect, with emphasis on the n π (O)—α * (P-axial substituent) interaction, provides the basis for rationalizing conformational preferences as well as geometrical details. Mean experimental geometries are compared to ab initio calculated geometries for conformers of (HO) 2 PH(O) and (HO) 2 PH(S) mimicking the dioxaphosphorinanes.

Ab initio studies of crystal field effects : part VIII. structure of formamide oxime using a 15-molecule cluster

Abstract The structure of formamide oxime in the crystal phase (P2 1 2 1 2 1 ) was completely optimised with standard gradient procedures using a 15-molecule cluster surrounded by point charges. The calculations were performed using 4-21G and 6-31G basis sets and in the SCF step of the calculations the MIA approach was used. Results are in better agreement with experimental results than a previous study, in which only point charges were used to model the crystal.

Vibrational analysis of different isomers of oxalyldihydrazide and the crystal structure of the “trans-trans” form

Abstract Laser Raman, IR, and far-IR spectra of different modifications of oxalyldihydrazide have been obtained and interpreted as a function of the presence of the cis secondary amide group. Assignments for the different structures are proposed and the crystal structure for the most stable conformer has been solved by X-ray diffraction. M r = 118.1; monoclinic; space group P 2 1 / c ; unit cell dimensions, a = 3.6188(3) A, b = 6.841(2) A, c = 9.133(2) A, β = 99.23(1)°, V = 223.2(1) A 3 ; Z = 2; D x = 1.76 g cm −3 ; Mo K α (λ = 0.71073 A); μ = 1.4 cm −1 ; F (000) = 62; T = 295 K. Final R -factor = 0.033; R w = 0.048, for 458 reflections with I > 3σ( I ) out of 531 measurements. The structure has been solved using MULTAN. The molecule is centrosymmetric and has a planar structure. The unusual geometry of the NH 2 groups is explained by intermolecular hyrogen bonding. Ab initio calculations, performed on four conformers of oxalyldihydrazide, reveal a large flexibility of the molecule which is also confirmed by the different vibrational spectra.

Transition metal complexes of singly and doubly deprotonated 2-thiooxamic acid

Abstract The new monomeric complexes trans -[M(HL) 2 (H 2 O) 2 ] (M = Mn, Co, Ni, Cd), trans -[M(HL) 2 ] · H 2 O (M = Pd, Pt) and [Hg(HL) 2 ] have been prepared together with the polymeric compounds trans -[ML(H 2 O)] n (M = Co, Ni, Zn) and trans-[PdL] n · 0.5nH 2 O (HL - and L 2- = the monoanion and dianion of 2-thiooxamic acid, respectively). The X-ray crystal structures of the manganese(II) and cadmium(II) complexes of HL - show a centrosymmetric octahedral geometry around the metal ion in both molecules. The ligand HL - behaves as a bidentate chelate with ligated atoms being the thioamide sulfur and one of the carboxylate oxygens. The room-temperature crystal structure of the known cis-[Zn(HL) 2 (H 2 O)] complex has also been determined and is compared with the previously published structure at 120 K. The complexes were characterized by elemental analyses, conductivity measurements, X-ray powder patterns, magnetic susceptibilities and spectroscopic (IR, far-IR, Raman, UV-vis) studies. The vibrational analysis of the complexes is given using OH/OD, NH/ND and metal isotopic substitutions. All data are discussed in terms of the nature of bonding and known and assigned structures. The dianion L 2− acts as a bis-bidentate O,N/O,S bridging ligand yielding square-planar (Pd II ) and octahedral (Co II , Ni II , Zn II ) polymeric compounds.