Experimental Charge Density Research Articles

Observation of a reversible isomorphous phase transition and an interplay of "σ-holes" and "π-holes" in Fmoc-Leu-ψ[CH2-NCS

Fmoc-Leu-ψ[CH2NCS] undergoes a reversible isomorphous phase transition upon cooling. The crystal structure at 100 K displays a short N=C=S···N=C=S intermolecular interaction, which has been characterized based on experimental charge density analysis, as a stabilizing interaction with both σ-holes and π-holes acting cooperatively.

Experimental validation of 'pnicogen bonding' in nitrogen by charge density analysis.

The participation of a nitrogen atom acting as an electrophile in pnicogen bonding, a hitherto unexplored interaction has been established by experimental charge density analysis. QTAIM and NBO analyses ratify this observation.

The effect of fatal carbon monoxide poisoning on the equilibria between cell membranes and the electrolyte solution.

The effect of fatal carbon monoxide poisoning on equilibria between cell membranes and surrounding ions was described using a theoretical four-equilibria model. The model was developed to obtain parameters characterizing the interactions between solution ions and erythrocyte or thrombocyte membrane surface. The parameters are the total surface concentrations of both acidic and basic groups C A, C B and their association constants with solution ions K AH, K BOH. These parameters were used to calculate the theoretical values of surface charge density. The model was validated by comparison of these values to experimental data, which were determined from the electrophoretic mobility measurements of the blood cells. The experimental and theoretical surface charge density values agree at pH 2–8, and at higher pH, the deviation was observed.

Electron-induced conversion of silylones to six-membered cyclic silylenes.

A silicon atom in the zero oxidation state stabilized by two carbene ligands is known as siladicarbene (silylone). There are two pairs of electrons on the silicon atom in silylone. This was recently confirmed by both experimental and theoretical charge density investigations. The silylone is stable up to 195 °C in an inert atmosphere. However, a substoichiometric amount (33 mol%) of potassium metal triggers the activation of the unsaturated C:Si:C backbone, leading to a selective reaction with a tertiary C-H bond in an atom-economical approach to form a six-membered cyclic silylene with three-coordinate silicon atom. Cyclic voltammetry shows that this reaction proceeds via the formation of a silylone radical anion intermediate, which is further confirmed by EPR spectroscopy.

Characterization of Interactions Involving Bromine in 2,2-Dibromo-2,3-dihydroinden-1-one via Experimental Charge Density Analysis

Experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one have been carried out to quantify the topological features of a short C–Br···O halogen bond with nearly linear geometry (2.922 Å, ∠C–Br···O = 172.7°) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the “σ-hole” on bromine, while the interaction energy is comparable to that of a moderate O–H···O hydrogen bond. In addition, the energetic contribution of C–H···Br interaction is demonstrated to be on par with that of the C–Br···O halogen bond in stabilizing the crystal structure.

First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate.

The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 Å(-1) with high completeness (89.1%; Rmrg = 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat and almost featureless. It was possible to derive reliable information on intermolecular interactions to model the anharmonic motion of a water molecule, and also to observe the fine details of the charge density distribution, such as polarization on O and H atoms involved in the strongest hydrogen bonds. When compared with our previous statistical study on oxalic acid data collected with the aid of CCD cameras, the complementary metal-oxide semiconductor (CMOS) detector can certainly be classified as a promising alternative in advanced X-ray diffraction studies.

Contributions of charge-density research to medicinal chemistry.

This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.

Probing systematic errors in experimental charge density by multipole and invariom modeling: a twinned crystal of 1,10-phenanthroline hydrate

The modeling of experimental electron density in a twinned crystal of 1,10-phenanthroline hydrate within an invariom approach revealed its another advantage for charge density studies, which is assessing the reliability of chemically relevant information provided by a conventional multipole refinement against high-resolution X-ray diffraction data.

Dithiadiazolyl Radicals—Structures and Charge Densities of Their Crystals and Co-Crystal

The results of experimental charge density studies on single crystals of two pure 1,2,3,5-dithiadiazolyl radical compounds (PhCN2S2, H-radical and C6F5CN2S2, F-radical) and their co-crystal (HF-radical) are presented. For all three cases, the use of anharmonic motions of the sulfur atoms (in the form of the Gram–Charlier expansion up to the third order) significantly improved the final refinement results. All of the above moieties form dimers in the crystal lattices of the studied compounds and have very similar geometrical parameters. The strength of the interactions in the dimers increases in the order: H-, F-, and HF-radicals, respectively. Calculated spin densities are almost entirely located on the nitrogen and sulfur atoms of the dithiadiazolyl rings, which results in a strong attraction between these molecular fragments in the dimers. Experimental electron density parameters obtained for all crystals are very consistent. The S–S bonds in all of the moieties have a partially shared character as conf...

Synchrotron charge density studies of chemical bonding in the polymorphs of FeS2

The experimental charge density (CD) distributions in both polymorphs of the photovoltaic compound iron-disulphide (FeS2; cubic pyrite and orthorhombic marcasite) will be described.[1] The CDs are determined by multipole modelling using synchrotron X-ray diffraction data collected at 10 K on extremely small single crystals (<10 mu) thus minimizing the influence of systematic errors such as absorption, extinction and TDS, and exploiting experiences gained from our recent synchrotron studies of CoSb3.[2] The analysis of the charge density in both polymorphs of FeS2 provides an opportunity to see how the different geometries affect local atomic properties, such as 2-center chemical bonding, atomic charges and d-orbital populations. In particular, the data and the resulting multipole models enable us to link the atomic-centered view that emerges from the multipole analysis with the band structure approach. This is carried out by combination with results from periodic calculations on the compounds in the experimental geometries using WIEN2k, thereby providing unambiguous answers to a number of unsolved issues regarding the nature of the bonding in FeS2. The chemical bonding will be characterized by topological analyses showing that the Fe-S bonds are polar covalent bonds, with only minor charge accumulation but significantly negative energy densities at the bond critical points. Using the IAM as reference, density is found to accumulate in-between the atoms, supporting a partial covalent bonding description. The homopolar covalent S-S interaction is seemingly stronger in pyrite than in marcasite, determined not only from the shorter distance but also from all topological indicators. Integrated atomic (Bader) charges show significantly smaller values than those estimation based on crystal-field theory of Fe2+, S-1. In connection with this, the experimentally derived d-orbital populations on Fe are found to deviate from the commonly assumed full t2g set, empty eg set, and they fit very well with the theoretical individual atomic orbitals projected density of states showing a higher dxy participation in the valence band in marcasite compared with pyrite. Thus, the differences between the two polymorphic compounds are directly reflected in their valence density distributions and d-orbital populations.

Experimental charge density studies of silver (I) complex

The antimicrobial [1] as well as antitumor activity of silver(I) complexes has been attributed to their interactions with nucleic acids, in the latter case preferentially with the bases rather than the phosphate groups [2]. The ability of silver(I) complexes to adopt structural diverse geometries with variable nuclearities , on the other hand, makes the study of silver(I) chemistry very attractive [1]. In the course of our studies of silver complexes with thioamide ligands we have determined the experimental charge density distribution in new silver(I) bromide complex with 2-mercaptobenzothiazole (mbztH) and triphenylphosphine (tpp) [AgBr(tpp)2(mbztH)], which allowed us to study e.g. the transfer of electron density to the bonding regions and the detailed analysis of different intra- and intermolecular interactions. In view of strong anticancer activity for MCF-7 (IC50 1.7510.25 μM) [3] of (1) and its sulfur containing ligand, this structure can be very interesting. Moreover the structure of (1) contains two independent complex molecules in asymmetric part of the unit cell, which together with the charge density description of mbztH and tpp allowed us to study different transferability approaches.

Charge Density Study of two Ni(III) and Ni(II) complexes

Experimental charge density of two nickel complexes with oxidation state +3 and +2 of composition (CH3(Ph)3P)+[Ni(bdtCl2)2]-, C31H22Cl4S4P1Ni1 [I] and (CH3(Ph)3P)+[Ni(bdtCl2)2]- dimethylsulfoxide solvate, C25H20Cl2S2P1Ni0.5; C2H6SO [II], (bdtCl2 = 3,6-dichloro-1,2-benzenedithiole ), has been studied. The coordination of Ni central atom by bdtCl2 as a non-innocent ligand gives rise to interesting electronic properties. Compounds I and II crystalize in a monoclinic space groups P 21/c and II in P 21/n, respectively. Their coordination is square-planar with the chromophore [NiS4]. Obvious differences for interatomic distances in metallocycles were found. For I in Ni1-S1-C1-C6-S2-Ni1 there are bond lengths of 2.1534(1), 1.7375(5), 1.4144(8), 1.7327(5), 2.1432(1) Å; and in Ni2-S3-C7-C12-S4-Ni2 there are bond lengths of 2.1453(1), 1.7390(5), 1.4133(7), 1.7387(5), 2.1523(1) Å. For II in Ni1-S1-C1-C6-S2-Ni1 there are bond lengths of 2.1776(2), 1.7437(8), 1.4169(11), 1.7431(8), 2.1663(2) Å. Significantly longer distances for II are in good agreement with the lower oxidation state of central atom. Very accurate data for I an II complexes were obtained with Oxford Diffraction CCD GEMINI R diffractometer at 100K. Multipolar refinement and consecutive topological analysis was performed using XD package. Differences in distribution of electron density in both complexes will be disscussed and compared with quantum-chemical calculations at BP86/VTZP level of theory [1]. This work has been supported by Slovak Grant Agency APVV and VEGA (APVV-0202-10 and 1/0679/11).

Experimental Charge Density studies of Ge(II) complexes using beamline I19

Interest in the p-block elements has recently been stimulated by the need for new reagents for materials and electronics applications, as well as the intrinsic interest in the unprecedented structures and properties observed. For germanium the development of low-valent compounds, organometallics, multiply bonded species, radicals and clusters is of significant importance. We have probed the coordination chemistry of Ge(II) with a range of neutral ligands, few examples of which were reported until recently. They exhibit many striking features including diverse structural motifs and highly variable coordination numbers (between 3 and 8) [1] suggesting the Ge centre does not to have a strong stereochemical preference and small differences in steric and electronic properties of the donor ligands have a significant role. Bonding models have been used to rationalise the observed structures with a Ge-based lone pair occupying the stabilised Ge 4s orbital. However these models are not entirely satisfactory and experimental charge density studies could provide valuable insights into the structures and chemistry of these compounds. [GeCl2(2,2'-bipyridine)], 1, and [GeCl2(1,2-bis(dimethylphosphino)benzene], 2, were selected as targets for initial experimental charge density studies and data have been collected using 3 different experimental configurations of the small molecule single-crystal diffraction beamline I19 [2] at Diamond Light Source. Using a Rigaku Saturn 724+ CCD detector on a 4-circle kappa-geometry CrystalLogic goniometer, data for 1 were collected at λ=0.6889Å without bimorph focussing mirrors in place, and for 2 data were collected at both λ=0.6889Å with bimorph mirrors and λ=0.4859Å without mirrors giving data to 0.48 and 0.38 Å resolution respectively. Details of the analysis of the topology of the electron density will be presented with the insights gained into the bonding in these unusual complexes.

Supramolecular Stark Effect in Host-Guest Complexes via Charge Density Analysis

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.

Charge density study of the first mixed-valent tetraphosphete

The first λ3,λ5-tetraphosphete contains a 4π-electron four-membered ring as the central structural unit of a dispirocyclic system and can thus be classified as an analogue to diphosphetes and cyclodiphosphazenes. According to its crystal structure the central P4unit exhibits not only P–P bonds which are of equal length (P1–P2 2,139(1) Å, P1–P2A 2,142(1) Å), but also rhombic distortion (P1–P2–P1A 79,4(1)0, P2–P1–P2A 100,6(1)0).[1] Therefore its electronic structure cannot be described as 'Phosphacyclobutadiene' but either as a bis(ylide) or as a system with delocalized double bonds. After various quantum chemical calculations and an extensive examination of its reaction and coordination behavior failed to answer this question, we addressed the problem via a detailed analysis of its charge density distribution. The experimental charge density based on high resolution X-ray diffraction data collected at low temperature is determined by multipole least squares refinement using the program packageXD2006.[2] In a first step, the static deformation density exhibits charge density which is located mainly outside of the P4ring plane at the λ3-phosphorus atoms but simultaneously redistributed into the P–P bond area. In addition to that, a study of its topological properties and an inspection of the Laplacian of the electron density according to Bader's `Quantum Theory of Atoms in Molecules' (QTAIM)[3] further highlight the bonding features. They reveal polar Si–N, Si–C and P–N bonds with a decreasing amount of electrostatic contribution as well as four valence shell charge concentrations (thus sp3hybridization) at each of the phosphorus atoms. Finally supported by theoretical calculations, the results illustrate the unique bonding situation in the P4unit combining a high ylidic character with unusual not exclusively sigma-like P–P bonds.

Experimental charge density studies: Discard valid data and overfit?

In experimental charge density investigation it is indispensable to use the highest possible quality of data. Therefore the multiplicity should be as high as possible, but poor data should be omitted. To decide about resolution limit and discarding outlier data often limits for Rint or I/σ(I) are used. A better approach is the `paired refinement method' [1] comparing two data sets by the fit of the models derived by the same refinement protocol to both data sets. For macromolecular data sets it could be shown that a higher resolution should be used than normally derived from the above mentioned criteria. First results for charge density data seem to show the same tendency but of course on a different level. The paired refinement strategy can also be used to investigate the influence of different scaling methods. In a recent version of SADABS [2] a new error model and a 3λ correction is implemented. With the paired refinement strategy the improvement in data quality gets obvious. A further concern in charge density investigation is the question of overfitting. In macromolecular refinement this is answered by the Rfree concept [3]. Here a refinement protocol is developed by refining against a work set of reflections, e.g. 90 % of the data. The remaining reflections are untouched in the whole refinement process but an Rfree value is calculated using only this test set of reflections. An overfitting can clearly be identified by a decrease in Rwork but an increase in Rfree. This refinement protocol is then used for a final refinement against all data. It will be discussed how this method could support charge density studies.

X-ray and neutron scattering: from ideal zeolites to real guest-host systems

Tetrahedral MOFs, microporous metallophosphates and zeolites share common framework topologies despite very different chemical nature of their crystalline skeleton. In the case of zeolites or metallophosphates, the polymeric [TO2]_ framework is based on single tetrahedral atoms T (T= Si4+/Al3+ or Ga3+/B3+/P5+ respectively) connected by corner oxygen atoms O. In the case of MOFs, the skeleton is built from supertetraedra formed by a central metal atom complexed by 4 organic linkers (terephtalate,...); hence homologous structures expanded by a "scale factor". In "molecular sieves", the static porosity but also the "breathing effect" control, in first approximation, the adsorption and the self-diffusion of guest molecules. These latter are finely tuned by the interaction of these molecules with the framework itself (though H-bonds or electrostatic interactions), with charge compensating cations in basic zeolites (through coulombic interaction), or with other adsorbed molecules. However, the interplay between guest molecule adsorption, framework relaxation, cation redistribution and atomic charge transfer leads to an inextricable problem for the modeling and prediction of adsorption properties in these systems in absence of any polarizable and adaptive force field. We will present experimental charge density studies on activated industrial zeolites FAU, MFI and MOR. The electrostatic properties derived on these systems (electric field, atomics charges) are validated by a comparison with those derived, experimentally and theoretically, on a comprehensive set of simpler quartz-type materials (SiO2, AlPO4, GaPO4,...) representative of typical microporous compositions. Finally, we will combine the informations brought by diffraction, diffuse scattering and Monte-Carlo modelling to analyse the adsorption process or the role of the template in the stabilisation of the framework in these systems and in the famous MIL-53 MOF

Combined Experimental and Computational Studies of Pyrazinamide and Nicotinamide in the Context of Crystal Engineering and Thermodynamics

Pyrazinamide and nicotinamide constitute small, rigid molecules, which are of importance in several areas of science, including crystal engineering, chemical synthesis, biochemistry, and pharmacy. This contribution is dedicated to the comprehensive study of experimental charge density distributions and computational analysis of the β form of pyrazinamide and α form of nicotinamide. Static electron density distribution is obtained through application of Hansen and Coppens multipolar formalism, and further analyzed via Bader’s quantum theory of atoms in molecules (QTAIM). Geometrical and electron density features of both crystals, such as atomic charges, bond critical points, electrostatic potential and experimentally derived intermolecular interactions are described and compared. The presence of the additional nitrogen atom in the aromatic ring of pyrazinamide, when compared to nicotinamide, has, as expected, a major influence on the surrounding atoms, including the amide moiety (0.2 e difference on the ca...

ChemInform Abstract: Probing the Zintl—Klemm Concept: A Combined Experimental and Theoretical Charge Density Study of the Zintl Phase CaSi.

AbstractThe nature of the chemical bonds in the Zintl phase CaSi is investigated by a combined experimental and theoretical charge density analysis to test the validity of the Zintl‐Klemm concept.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.