Progress in detection of and correction for low-energy contamination.

Contamination with low-energy radiation leads to an increased number of weighted residuals being larger in absolute terms than three standard uncertainties. For a Gaussian distribution, these rare events occur only in 0.27% of all cases, which is a small number for small- to medium-sized data sets. The correct detection of rare events - and an adequate correction procedure - thus relies crucially on correct standard uncertainties, which are often not available [Henn (2019), Crystallogr. Rev. 25, 83-156]. It is therefore advisable to use additional, more robust, metrics to complement the established ones. These metrics are developed here and applied to reference data sets from two different publications about low-energy contamination. Other systematic errors were found in the reference data sets. These errors compromise the correction procedures and may lead to under- or overcompensation. This can be demonstrated clearly with the new metrics. Empirical correction procedures generally may be compromised or bound to fail in the presence of other systematic errors. The following systematic errors, which were found in the reference data sets, need to be corrected for prior to application of the low-energy contamination correction procedure: signals of 2λ contamination, extinction, disorder, twinning, and too-large or too-low standard uncertainties (this list may not be complete). All five reference data sets of one publication show a common resolution-dependent systematic error of unknown origin. How this affects the correction procedure can be stated only after elimination of this error. The methodological improvements are verified with data published by other authors.

On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model.

X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

Diferrocenyl Thioketone: Reactions with (Bisphosphane)Pt(0) Complexes-Electrochemical and Computational Studies.

Diferrocenyl thioketone reacts smoothly with (bisphosphane)Pt(0) complexes in toluene solution at room temperature yielding 1:1 adducts identified as ferrocenyl (Fc) functionalized platinathiiranes. Their structures were unambiguously confirmed by means of spectroscopic methods as well as by X-ray diffraction analysis. A unique, ferrocene-rich platinathiirane, bearing three Fc-units, was prepared starting with [bis(diphenylphosphino)ferrocene] Pt(0(η2-norbornene). For comparison, a similar platinathiirane with one Fc-unit was obtained from the reaction of the latter complex with thiobenzophenone. Quantum-chemical calculations were carried out to describe the bonding pattern and frontier molecular orbitals of the ferrocene-rich platinathiirane complexes. These calculations confirmed that the C=S bond loses its formally double-bond character upon complexation (bisphosphane)Pt(0). Cyclic voltammetry measurements were performed to characterize the obtained platinathiiranes in CH2Cl2 solutions. For comparison, the cyclic voltammogram for diferrocenyl thioketoneas a mixed-valent (FeII-FeIII) compound was also recorded and analyzed. The results point out to a diffusion controlled electrode process in case of differocenyl thioketone and mixed diffusion and adsorption controlled electrode process in the case of the studied platinathiiranes.

[3]rotaxanes composed of two dibenzo-24-crown-8 ether wheels and an azamacrocyclic complex.

The azamacrocyclic complex was used as a platform for the construction of [3]rotaxanes containing two DB24C8 macrocycles per molecule. The complex unit incorporates two electron deficient π-bond systems and two N-H hydrogen bond donating groups which facilitated the formation of a 1 : 2 interlocked structure. Synthesis and properties of such compounds are presented. Structures of the obtained compounds were confirmed by NMR spectroscopy, ESI mass spectrometry, elemental analysis and single crystal X-ray diffraction. Both [3]rotaxanes containing two DB24C8 macrocycles per molecule crystallise in P1[combining macron] and P21/n space groups. They have different counterions (PF6- and Cl- anions, respectively) and mostly disordered solvent molecules such as water, methanol and acetone. Both [3]rotaxanes have a flexible axle in which the Cl- salt takes the shape closer to the "S"-letter, while in the PF6- case the axle is more linear. The shape results from respective packing and intra-, and intermolecular interactions among the moieties in the rotaxane and the crystal lattice.

Regioselective Functionalization of the [ closo-1-CB9H10]- Anion through Iodonium Zwitterions.

Reactions of [ closo-1-CB9H9-1-R]- (2, R = H, COOH, C5H11) with PhI(OAc)2 lead to mixtures of regioisomers [ closo-1-CB9H8-1-R-6-IPh] (5[6]) and [ closo-1-CB9H8-1-R-10-IPh] (5[10]) in ratios of ∼3:1 to 1:1, of which the former isomer undergoes selective reactions with nucleophiles (MeCN, pyridine, MeC(═NH)NH2, CN-). The products and the unreacted 10-isomers 5[10] are separated achieving kinetic resolution of the isomeric iodonium zwitterions. Pure 5[10] is reacted with nucleophiles (pyridine, 4-C7H15OPyridine, Me2NCHS, PhCO2-, CN-, N3-, I-, MeC(═NH)NH2, and MeCN), giving substitution products. The mechanism of the substitution is investigated with density functional theory (DFT) methods. Some of the nucleophilic substitution products are transformed further, expanding the scope of available functional groups for the [ closo-1-CB9H10]- anion. Four derivatives are characterized with single-crystal XRD methods: [ closo-1-CB9H9-10-N2] (4[10]a), [ closo-1-CB9H9-6-NC5H5] (9[6]a), [ closo-1-CB9H9-10-NC5H5] (9[10]a), and [ closo-1-CB9H9-10-NHC(NH2)Me] (10[10]a). Spectroscopic data for selected derivatives are interpreted in terms of transmission of electronic effects through the { closo-1-CB9} cluster (NMR) and interaction with substituents (IR, UV). The latter results are compared to those of TD-DFT computational methods.

Magnetostructural Investigation of Orthogonal 1-Aryl-3-Phenyl-1,4-Dihydrobenzo[e][1,2,4]triazin-4-yl Derivatives.

3-Phenyl-1,4-dihydrobenzo[e][1,2,4]triazinyl radicals with the N(1) position substituted with naphth-2-yl (1 b), naphth-1-yl (1 c), pyren-1-yl (1 d), anthracen-9-yl (1 e), 2-trifluoromethylphenyl (1 f), 3-trifluoromethylphenyl (1 g), and 2-iodophenyl (1 h) were characterized by using single-crystal X-ray diffraction, variable-temperature magnetic susceptibility, and DFT computational methods. The substituent at N(1) is essentially orthogonal to the heterocycle plane in 1 f and 1 h, and with a high torsion angle in 1 c and 1 d. Radicals 1 c and 1 h form unusual infinite chains with crisscrossing hetero-co-facial π-π interactions, whereas radical 1 d forms analogous homo-co-facial arrangements. Infinite chains of homo-co-facial π-π dimers are found in 1 b, 1 f and 1 g; in the latter the position of the CF3 group controls the slippage of the dimers in the chain. No π-π parallel arrangements were found in 1 e. Magnetic susceptibility measurements demonstrated strong antiferromagnetic interactions in 1 b (J=-264±4 cm-1 ) and 1 f (J=-134±1 cm-1 ), while weak intradimer ferromagnetic interactions were found in 1 g (J2 =+21±1 and J1 =-15±1 cm-1 ). Other derivatives exhibit typical weak antiferromagnetic exchange interactions in a range of -5 to -10 cm-1 .

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Synthesis and characterization of 12-pyridinium derivatives of the [closo-1-CB11H12]- anion.

Diazotization of [closo-1-CB11H10-1-R-12-NH2](-)[NMe4](+) (4[NMe4]) in neat 4-methoxypyridine leads to 12-(4-methoxypyridinium) zwitterions [closo-1-CB11H10-1-R-12-(4-MeOC5H4N)] (2) in ∼50% yield. Demethylation of 2 with LiCl in dimethylformamide provides access to 12-pyridones 5[NMe4], which can be O-alkylated with alkyl triflates giving 12-(4-alkoxypyridinium) zwitterions, such as 1. This three-step process is more efficient than direct diazotization of amine 4[NMe4] in neat higher 4-alkoxypyridine. The new method was demonstrated for the synthesis of [closo-1-CB11H10-1-C5H11-12-(4-C7H15OC5H4N)] (1c), which exhibits a smectic A phase. Molecular and electronic structures of 4-methoxypyridinium zwitterion 2b and its C(1) isomer [closo-1-CB11H11-1-(4-MeOC5H4N)] (3b) were investigated by single-crystal X-ray diffraction and spectroscopic methods, respectively, and the experimental results were compared to those obtained with density functional theory methods. Lastly, the mechanism for formation of zwitterions 2 was investigated computationally revealing low energy for dediazoniation of the [closo-1-CB11H10-1-R-12-N2] (14) intermediate (ΔG298 ≈ 25 kcal/mol) to form boronium ylide 15, with weak dependence on substituent R. Dinitrogen derivative 14c was observed by (11)B NMR spectroscopy.

A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers.

Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ≈ 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ≈ 0.93 on average). The RSMEs do not exceed 3.2 kcal mol-1 for the UBDB and are in the range of 3.7-7.6 kcal mol-1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications to macromolecules.

Statistical analysis of multipole-model-derived structural parameters and charge-density properties from high-resolution X-ray diffraction experiments.

A comprehensive analysis of various properties derived from multiple high-resolution X-ray diffraction experiments is reported. A total of 13 charge-density-quality data sets of α-oxalic acid dihydrate (C2H2O4·2H2O) were subject to Hansen-Coppens-based modelling of electron density. The obtained parameters and properties were then statistically analysed yielding a clear picture of their variability across the different measurements. Additionally, a computational approach (CRYSTAL and PIXEL programs) was utilized to support and examine the experimental findings. The aim of the study was to show the real accuracy and interpretation limits of the charge-density-derived data. An investigation of raw intensities showed that most of the reflections (60-70%) fulfil the normality test and the lowest ratio is observed for weak reflections. It appeared that unit-cell parameters are determined to the order of 10(-3) Š(for cell edges) and 10(-2) ° (for angles), and compare well with the older studies of the same compound and with the new 100 K neutron diffraction data set. Fit discrepancy factors are determined within a 0.5% range, while the residual density extrema are about ±0.16 (3) e Å(-3). The geometry is very well reproducible between different data sets. Regarding the multipole model, the largest errors are present on the valence shell charge-transfer parameters. In addition, symmetry restrictions of multipolar parameters, with respect to local coordinate systems, are well preserved. Standard deviations for electron density are lowest at bond critical points, being especially small for the hydrogen-bonded contacts. The same is true for kinetic and potential energy densities. This is also the case for the electrostatic potential distribution, which is statistically most significant in the hydrogen-bonded regions. Standard deviations for the integrated atomic charges are equal to about 0.1 e. Dipole moments for the water molecule are comparable with the ones presented in various earlier studies. The electrostatic energies should be treated rather qualitatively. However, they are quite well correlated with the PIXEL results.

An improved experimental databank of transferable multipolar atom models--ELMAM2. Construction details and applications.

ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.

Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases.

The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high-resolution single-crystal X-ray diffraction experiment on L-His-L-Ala dihydrate and 23 K high-resolution data for L-Ala [Destro & Marsh (1988). J. Phys. Chem. 92, 966-973], the structural properties, electron-density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal-field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly-L-His dihydrate, D,L-His and the above-mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root-mean-square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X-H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high-resolution and low-resolution data, respectively. Differences in dipole-moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9-15 and 22-33 kJ mol(-1) for UBDB and the other database models, respectively.

Structural analysis and multipole modelling of quercetin monohydrate--a quantitative and comparative study.

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

X-ray diffraction, FT-IR, and (13)C CP/MAS NMR structural studies of solvated and desolvated C-methylcalix[4]resorcinarene.

Solid C-methylcalix[4]resorcinarene solvated by acetonitrile and water (CAL-Me) and then modified by slow solvent evaporation (CAL-Me*) was studied using single-crystal and powder X-ray diffraction, FT-IR, and (13)C CP/MAS NMR. The CAL-Me solvate crystallizes in the monoclinic P2(1)/n space group with three CH(3)CN and two H(2)O molecules in the asymmetric part of the unit cell. The CAL-Me molecules adopt a typical crown conformation with all of the hydroxyl groups of the aryl rings oriented up and all of the methyl groups disposed down (the rccc isomeric form). The crystalline network is formed by resorcinarene, CH(3)CN, and H(2)O molecules and assembled by intermolecular hydrogen bonds and weak C-H...A or C-H...pi interactions. The desolvated CAL-Me* loses its crystalline character and becomes partly amorphous. It is devoid of CH(3)CN and deficient in water. However, the resorcinarene molecules still remain in the crown conformation supported by intramolecular hydrogen bonds, while intermolecular hydrogen bonds are considerably disintegrated. The work directs general attention to the problem of stability and polymorphism of resorcinarene solvates. It shows that the joint use of diffractometric and spectroscopic methods is advantageous in the structural studies of complex crystalline macromolecular systems. On the other hand, the solid-state IR and NMR spectroscopic analyses applied in tandem have been found highly beneficial to elucidate the disordered structure of poorly crystalline, desolvated resorcinarene.

Determination of experimental charge density in model nickel macrocycle: [3,11-bis(methoxycarbonyl)-1,5,9,13-tetraazacyclohexadeca-1,3,9,11-tetraenato-(2-)-kappa(4)N]nickel(II).

Experimental and theoretical atomic charges and d-orbital populations were obtained for [3,11-bis(methoxycarbonyl)-1,5,9,13-tetraazacyclohexadeca-1,3,9,11-tetraenato(2-)-kappa(4)N]nickel(II) monocrystal (16Ni) using the Hansen and Coppens formalism. Several models of this structure were tested as a function of quality of the fit, convergence of the refinement, value of residual peaks and holes, and Hirshfeld's rigid-bond test. The models with Ni-atomic scattering factors applied for the metal center are significantly better than those with the Ni-ionic scattering factors. The properties of the final electron density distributions are very consistent and similar for all of the models tested. The values of the d-orbital populations for Ni roughly agree with the occupation order of the d-electron levels for square-planar complexes derived from crystal field theory and are comparable with those obtained by the natural population analysis method. Experimental atoms-in-molecules charges calculated for four different models agree quite well for models with different symmetry restrictions and the same scattering factor for the Ni. Both experimental and theoretical methods predict relatively high negative values of charges for the nitrogen and oxygen atoms and also a quite high positive charge for the C(7) atom. The values of rho(r(BCP)) for the Ni-N bonds are in the range from 0.60 up to 0.75e A(-3), with positive laplacian values indicating noncovalent bonding. For the laplacian of the electron density evaluated in the plane of the macrocyclic ring, a typical map for a square-planar complex was obtained with four charge concentrations--3d(xy) orbitals--pointing toward the regions between the M-N bonds and charge depletions directed toward the (3,-1) critical points of the negative laplacian for the nitrogen atoms.

Neutral nickel(II) and copper(II) tetraazamacrocyclic complexes as molecular rods attached to gold electrodes.

New dithiolated derivatives of neutral Cu(II) and Ni(II) tetraazamacrocyclic complexes have been synthesized and characterized by spectroscopic and diffractional methods. These rod-shaped molecules were assembled in monocomponent and mixed monolayers on gold electrodes. In the mixed monolayers, the active molecules were embedded in a hexanethiol matrix. The dithiolated complexes are oriented perpendicularly to the electrode, and reveal faster kinetics of electron transfer than those assembled in a single-component monolayer. They appear as protrusions, which are easily addressed by using the STM method. In the presence of a suitable electron acceptor in the solution, the donor properties of the anchored Cu complex were weakened, which revealed donor-acceptor interactions with the monolayer. The peak position in the voltammogram indicates a stronger interaction of the solution-based acceptor with the reduced Cu(II) form than with the Cu(III) complex. This suggests the possibility of switching the association on or off by applying an appropriate potential.

Fine-tuning of properties of bismacrocyclic dinuclear cyclidene receptors by N-methylation.

N-Methylated bismacrocyclic Cu and Ni complexes were synthesised and structurally characterised in the solid state. Their properties in solution were analysed by using NMR and ESR spectroscopies and electrochemical methods. Face-to-face biscyclidenes linked through polymethylene chains form rectangular boxlike cations. These moieties can host some small guest molecules (water, pi-electron donating compounds) and are stabilised by a shell of neighbouring counterions. For the bismacrocyclic dinuclear complexes containing two nickel or two copper ions, the intramolecular interactions between the metallic centres are strengthened through methylation of the macrocyclic components, as compared with the nonmethylated species. We report the electron coupling created by two unpaired electrons coming from two copper centres observed by ESR spectroscopy. Methylation weakens the electron-acceptor properties of the complexes, which leads to less effective binding of the pi-electron-donating guests. It also increases the stability of the lower oxidation states. In the case of the copper complexes, both Cu(II)/Cu(I) and Cu(II)/Cu(III) reversible one-electron transfers are seen in the voltammograms. These changes in properties are interpreted as the consequences of steric repulsion between the methyl substituents and the macrocyclic ring.

Intermetallic interactions in face-to-face homo- and heterodinuclear bismacrocyclic complexes of copper(II) and nickel(II).

New face-to-face heterodinuclear complexes containing copper(II) and nickel(II) in identical tetraazamacrocyclic environments have been synthesized and characterized using ESI mass-spectrometry, X-ray diffraction, spectroscopic methods, and elemental analysis. These new bismacrocyclic systems were compared with the respective mono- and bismacrocyclic and [2]catenane homonuclear complexes. Interactions between the metal centers were monitored by magnetic and electrochemical measurements. Magnetic data indicate that all copper compounds studied behave as weakly interacting magnets. In the case of copper [2]catenane, the extent of magnetic interactions decreased when a benzocrown moiety was introduced between the macrocyclic units. On the basis of electrochemical data, the interactions between the metal centers were found to be substantially larger for the nickel complexes than for the corresponding copper ones. Interlocking of a benzocrown ether to form [2]catenane led to a nonequivalence of the metal centers and to the increase of donor abilities of the catenane compared to the respective bismacrocyclic complex. This is reflected by the shift of the first formal potential to less positive values. Intermetallic interactions for the heteronuclear nickel/copper complexes were found intermediary compared to the homonuclear ones. They were strengthened by shortening the spacer between the two tetraazamacrocyclic subunits which is a convenient way of fine-tuning the interactions. The increase of intermetallic interactions led to the increased stability of the intermediate mixed-valence states indicated by the higher values of comproportionation constants.